Surveys have shown the race tightening to a statistical dead heat, with incumbent governor Basuki "Ahok" Tjahaja Purnama, an ethnic Chinese Christian, closing in on rival Anies Baswedan, a former education minister.
A day after suffering electoral defeat, Basuki Tjahaja Purnama - commonly referred to as Ahok - fronted court in Jakarta to hear the demand by prosecution over allegations he insulted the Koran during a speech in September a year ago, in which he talked about how his detractors had used a Koranic verse to persuade people not to vote for a non-Muslim.
In the months prior to the election, Baswedan had appeared to pull away from Basuki Tjahaja Purnama, commonly called Ahok, but a series of corruption allegations levelled at the academic-turned-agitator in March had opinion polls showing the two candidates neck-and-neck before today's vote.
Some voters may have been reluctant to vote for Purnama because of worries about "five more years of protests on the streets by Muslim hardliners", Loveard said in a telephone interview.
Tensions have risen since the first round of voting on February 15, when Ahok came in first with nearly 43% of the vote, just ahead of former Education and Culture Minister Anies Baswedan. However, when a non-Muslim of Chinese descent desires a leading role (such as the position of Jakarta governor), there emerges fierce opposition from this hardline Islamic group.
Hardline Islamic cleric Habib Rizieq, who helped organise the anti-Purnama demonstrations during the campaign, last week urged Muslims to travel to Jakarta and be ready to "finish" their opponents.
The campaign has been "the dirtiest, most polarising and most divisive the nation has ever seen", the Jakarta Post said in an editorial on Tuesday.
The early count was done by private pollsters endorsed by election officials.More news: Bill O'Reilly Out At Fox News
Ahok's loss may make it harder for President Joko Widodo, who handed over the governorship to him after he took the top job in the country in 2014.
Citigroup said in an investor note that, despite the potential for renewed protests if Purnama won, it was maintaining a Jakarta stock index target of 6,150 by the end of 2017, representing an 8 percent upside.
"The police should remain proportional [in deploying officers] and not make the security too conspicuous, so that people will feel comfortable when they vote", Dahliah said. "The blame is on the politicisation of religion, not Jakarta voters", he told AAP. "So much can change so quickly here", said Ian Wilson, research fellow at Australia's Murdoch University Asia Research Center.
Purnama won the first round of voting in February in a three-way race with 43 percent of the ballots to set up Wednesday's second round with Basedan, who won 40 percent. Prabowo is expected to challenge Widodo again in 2019.
Prosecutors said it was clear Ahok had been "disappointed" that Indonesia's "political elite" had used the Koranic verse Al-Maidah 51 against him, in a bid to persuade voters not to elect a non-Muslim.
Hundreds of members of the hardline Islamic Defenders Front (FPI) rallied outside the court, chanting "not enough" after the prosecution made their request.
Just how Uno, who will be deputy governor if elected, and Baswedan, the governor hopeful, closed the gap on Ahok and his running mate Djarot Saiful Hidayat is up for debate.
Widodo, who grew up in a shack by a river in rural Java and became a successful furniture seller before entering politics, was the insurgent candidate who defeated Prabowo in the 2014 presidential election.