As the extent of Jakarta governor Basuki Tjahaja “Ahok” Purnama’s crushing election defeat became clear on Wednesday afternoon, one refrain among the hard-headed administrator’s many admirers was, “Poor Ahok”.

“Poor Ahok?” a usually taciturn Indonesian acquaintance responded. “Poor Jakarta, you mean. Poor Indonesia.”

In a country whose national dictum for 70 years has been Unity in Diversity, the key themes in the ugly political contest to rule its capital city were inescapably race and religion.

More specifically it was the fact that the now outgoing governor, as an ethnic Chinese Christian, was the wrong race and ­religion.

An election victory for Ahok would have said much about the commitment of Australia’s closest Asian neighbour — a country so frequently referred to as a moderate Muslim nation that it has become something of a cliche — to its foundational principles.

There was no candidate to rival the 50-year-old’s administrative skills, nor his record as the most effective and graft-free governor this city of 10 million residents has seen in decades. The few reliable polls there were reflected as much though, in an apparently worldwide trend, they failed to predict the margin of Ahok’s loss.

Instead his defeat is a triumph for Indonesia’s previously fringe Islamist groups and hardline clerics who led the push for his ouster, as much as it is for man who won the election, Anies Baswedan.

While election-eve polls had the two candidates running neck and neck, the unofficial post-election count (the official result will not be made public until May 1) showed Anies and his running mate Sandiaga Uno captured about 58 per cent of the vote.

Australian National University Indonesia expert Marcus Mietzner says the Jakarta result reflects the growing power of those once-marginal Islamist groups to swing elections in Indonesia.

Issues that should have been central to the campaign — Jakarta’s perennial flooding problems, education and healthcare, a desperately needed antidote to the crowded city’s chronic traffic issues — were overshadowed by debate over whether a Muslim-majority city should be governed by a non-Muslim.

Ahok’s lighthearted questioning of the Koranic verse conservative clerics claimed underpinned their edict forbidding such a political scenario gave his detractors the ammunition they needed against him.

The al-Maidah 51 verse, historically subject to varying interpretations, is regularly cited by Indonesian Islamists when a non-Muslim seeks public office.

Ahok has faced it his entire political career. But this time it proved his undoing, opening the door to what now seems a likely conviction for blasphemy.

Mietzner says otherwise moderate Muslims were persuaded by a “relentless grassroots, mosque-based and social media campaign that (a) Ahok was unelectable, and (b) anyone still voting for him was a bad Muslim”. In the last weeks of the campaign thousands of banners appeared across the city warning Ahok supporters would be denied Muslim burial rights.

“There is no doubt in my mind that the politicisation of Ahok’s religion (wrapped in the blasphemy issue) was the single most important factor deciding this election,” he concludes in an analysis shared with The Australian.

“And this politicisation was driven by the increasing capacity, mobilisation and outreach of ­Islamist groups, who formed an effective alliance with Ahok’s challengers.”

In a brief victory speech on Wednesday night, governor-elect Anies vowed to unify and work for all Jakartans, regardless of their race or religion, and to heal the wounds of a divisive campaign.

“We are committed to preserving diversity and unity,” he said. “We aim to make Jakarta the most religiously harmonious pro­vince in Indonesia.”

Ahok, graciously, also called on his supporters to “forget all of the problems faced during the campaign because Jakarta is home for all of us”.

But it may be too late for that. Even as Anies was promising unity and healing, at his campaign headquarters on Wednesday night speeches were made lauding the defeat of the “Chinese governor”.

“Now we have won the election and defeated the Chinese governor … we have more chance to ­implement what we want,” Mohammed Saleh, a spokesman for paramilitary group PETA (Defenders of the Motherland), told ecstatic Anies supporters.

“This includes how to prioritise Indonesian people over foreigners, including Chinese.”

An ugly side effect of the campaign against Ahok has been more open racism towards Indonesians of Chinese descent, a group that sporadically has been subjected to discrimination and violence.

Offensive racial epithets to describe Ahok as well as Chinese-Indonesians more generally have proliferated on social media networks in the past six months.

Anies, a former education minister and Fulbright scholar, paraded his Muslim credentials throughout the campaign and pandered to the vigilante Islamic Defenders Front (FPI), which led three massive rallies in Jakarta last year calling for Ahok’s political scalp and his jailing for blasphemy.

Prosecutors in Ahok’s blasphemy trial yesterday demanded he serve a two-year probation for having incited social unrest by insulting the Koran, but serve a year in prison for any breach of that probation. The verdict and his sentence are expected to be handed down within weeks.

While the downfall of one Asian city mayor may not seem particularly momentous, what Ahok’s defeat says about political trends in Indonesia is important.

“What this shows is that you can appeal to racist and religious sentiments for election purposes, and every single politician in this country has seen that it works,” director of Melbourne University Centre for Indonesian Law, Islam and Society Tim Lindsey tells The Australian.

“Everybody is running around Jakarta trying to pretend everything is OK. But what this shows is it is quite all right to use religious chauvinism and mobilise mobs to intimidate in order to get a desired democratic outcome.

“Every (Indonesian) politician will be extraordinarily careful not to be at the wrong end of the mob, so will have to adopt the same values used so effectively against Ahok. That could signal a big shift in Indonesian democracy.” Future political campaigns will necessarily be run in a manner “less compatible with an open, liberal, pluralist society”, Lindsey predicts.

Although no one suggests Indonesia is sliding towards an Islamic state, there is general agreement the country is in the midst of an internal struggle over Islam’s position and influence.

And if, as seems likely on present trends, Islam is to play a greater social and political role, that will necessarily require a shift in how Indonesia’s neighbours deal with it, Lindsey adds.

Successive Australian governments have invested considerable energy in trying to build a closer relationship with Indonesia, and more recently an alliance that can influence regional policy and outcomes on issues from the South China Sea to trade and terrorism.

Malcolm Turnbull has had the most notable success of recent years, thanks to a much-mooted personal relationship with President Joko Widodo, popularly known as Jokowi in Indonesia, and at every chance has talked up the country’s regional leadership and its role as a moderate, democratic bulwark against Islamic extremism.

Indonesia is tipped to become the world’s fourth largest economy by 2045, making it a major player on the world stage. Yet Australia is only its 13th largest trading partner, with two-way annual trade in goods and services valued at just $15 billion and Australian direct investment in Indonesia of just $5.5bn in 2015-16..

Lindsey predicts, however, that Australia’s historical struggle to engage more closely with Indonesia is going to get a lot tougher.

“We live in an area where democracy is dysfunctional, or troubled at best, and we need to be a bit more clear-eyed about this,” he says.

“It’s clear some of the old, comfortable cliches about Indonesia have to be discarded and we need to take a more hard-headed, realistic approach to what’s going on,” Lindsey adds. “There’s been this very widely accepted view that Indonesia is the smiling face of Islam, but that has not really been true for some time,” he says, citing a sharp rise during the previous decade in blasphemy convictions and instances of intolerance.

“What we are seeing is a really open statement that these (Islamist) groups are here to stay and will play an important part in politics. This is a really big shift, given many of these people would undoubtedly have been locked up under Suharto.

“Now they’re mainstream political players.”

One of the nation’s key powerbrokers, Prabowo Subianto whose Gerindra Party backed Anies Baswedan’s bid for Jakarta governor, admitted as much Wednesday night, acknowledging the role of notorious FPI leader Rizieq Shihab and other Muslim clerics in the victory and calling on rivals to stop branding them as treasonous radicals.

Prabowo lost the 2014 presidential election to the reformist former Jakarta governor Jokowi, but Anies’s victory is seen to have put him squarely back in the race for the 2019 presidential elections, in which the incumbent is widely tipped to seek a second term.

The Jakarta elections were widely seen as a warm-up for the 2019 race, and the two candidates who squared off in this week’s second round of voting the proxies of the likely presidential contenders.

Ahok was deputy to Jokowi before the latter’s election to the presidency, and his candidacy was backed by Jokowi’s Democratic Party of Struggle (PDIP).

The conventional wisdom was that a win for Ahok would help Jokowi’s re-election bid, while a win for Anies would hand Gerindra the keys to Indonesia’s richest city, and Prabowo a significant boost should he choose to once again contest the presidency. Melbourne University’s Lindsey agrees that Anies’s win represents a “massive victory for Prabowo”.

“Everything that goes right in Jakarta from now on can be attributed to his candidate and Gerindra can claim the benefit in 2019,” he says.

“Everything that goes wrong in Jakarta can be attributed to Ahok, and thus Jokowi.

“A Prabowo presidency would mean a far more right-wing, authoritarian government, without question,” he adds of the former special forces commander who has been accused by human rights groups of links to war crimes in East Timor.

That’s not to say there will be no pushback against the Islamists’ march in Indonesia from powerful groups that do not like the direction in which the country appears to be heading.

The Indonesian military, for all its many faults, has historically championed pluralism over religious piety.

Indonesian rulers from Sukarno, the founding president of the independent nation, onwards have also valorised the principle of Unity in Diversity as a necessary tool for maintaining national cohesion.

Jakarta-based political analyst Kevin Evans says an important factor will be how the Jakarta election mobilises the pluralists to become more engaged and push back against creeping “Islamist primordialism”.

“If it energises the centre and left to start thinking seriously on these things, it wouldn’t be a bad thing,” he says.

Those closely watching the power dynamic in Indonesia say the charged political atmosphere — and the heightened backroom meetings now taking place among the country’s powerbrokers — is reminiscent of the activity in 1996 and 1997 that led to the downfall of the country’s long-term strongman, Suharto.

“I am not saying we are there yet,” one veteran Indonesia analyst said yesterday. “But for the first time there is a similar sense of unease.

“This is a very uncertain time, which is not a good thing in Indonesia.”

And an uncertain time in Indonesia is surely not a good thing for Australia.