The official result will not be known until early March but according to quick count results, which have proven accurate in the past, Ahok was narrowly leading Anies with 43 per cent of the vote after a peaceful polling day.

The embattled Ahok, who is fighting blasphemy charges that could see him jailed for up to five years, told his supporters the fight was not over yet.

"Three to four months ago there was a pollster who said that we could not make 20 per cent - one even said we would only get 10 per cent of the vote - but from the temporary count we are leading at number one," Ahok said.

Ahok's campaign team had desperately hoped he would win the February election outright, as the vote that had been split between the two Muslim candidates is expected to flow to Anies in an April run-off election.

"But what we know is that the spirit to support the Ahok-Djarot ticket will never die out," Ahok said. "We are grateful at least that there are still many people who believe in us, many people still see that we are capable of managing Jakarta for all.

The dark horse was Anies, who began to climb in the polls after solid debate performances and strategic courting of the Muslim vote - including a controversial visit to the Islamic Defenders Front HQ - which saw him poll about 39 per cent of the vote.

He also emphasised his opposition to land reclamation in Jakarta Bay and forced evictions, both controversial programs under Ahok's tenure that have alienated the urban poor.

Anies campaign was assisted by popular former military chief Prabowo Subianto, whose Gerindra party endorsed Anies and his running mate Sandiaga Uno, adding fuel to the theory that this fiercely contested election was a proxy war for the 2019 presidential election.

Prabowo, who was President Joko Widodo's rival in the 2014 presidential election, told a rally of hundreds of thousands in central Jakarta: "If you want me to be President in 2019, you must bring victory for Anies-Sandiaga."

On election day Prabowo said: "Today is the day we've been anticipating. Thank God we witness the revival of the movement of the Indonesian people because the Jakarta gubernatorial election has become the symbol of the fight between those who want justice, truth and honesty and those who want to prove that money can colonise all Indonesian people."

The election campaign was mired in sectarian tension. Ugly anti-Chinese and religious sentiment erupted in three mass rallies calling for Ahok to be jailed for blasphemy. He was labelled a pig, a dog and a kafir, the Islamic term for an infidel, with many arguing a non-Muslim should not lead Jakarta.

In a sweet victory for Ahok, he won the polling booth where his arch nemesis Rizieq Shihab - an Islamic hardliner who spearheaded the anti-Ahok rallies - cast his vote.

The third candidate, Agus Harimurti Yudhoyono, polled a disappointing 17 per cent after his campaign was derailed by poor debate performances and the embarrassing Twitter rants of his father, Susilo Bambang Yudhoyono, who was president of Indonesia from 2004 to 2014.

It is unknown what Agus will do next given he quit a promising military career to stand as governor, a move that surprised many because he was a political neophyte.

Australian National University Associate Professor Marcus Mietzner believes there are three main reasons why Anies' electability climbed while Agus' floundered.

"First, Agus performed badly in both the first and the second debate, while Anies appeared competent; second, Prabowo's grassroots campaign for Anies was effective, in contrast to SBY's creation of Twitter controversies and third, the conservative Muslim vote consolidated around Anies."

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