Purnama, an ethnic Chinese Christian backed by the ruling Indonesian Democratic Party of Struggle, conceded defeat and called for unity at a news conference in Jakarta. If he wins, Ahok will be the first non-Muslim directly elected to the post. His alleged blasphemy led to thousands of people protesting against his candidacy during the campaign.
Ahok was fiercely targeted during the campaign by hard-line Muslim groups, who supported Baswedan.
Indonesia is the world's most populous Muslim country, with an estimated 263 million people, about 87% of whom are followers of Islam. In this case, there may well have been concerns about the prospect of five years of street disturbances and a trial verdict that could have disqualified Purnama from assuming office anyway.
The controversy has clearly hurt Mr Purnama's chances.
Some 90% of the almost 7 million voters in Jakarta are Muslim.
Voting for Ahok seemingly does not come without threats or consequences.
Uno had said that his team would continue most of the central government's infrastructure projects in Jakarta.
"We believe that because Jakarta and Indonesia is majority-Muslim, it should be led by a Muslim", said Novel Bamukmin, head of the Jakarta chapter of the FPI.
Hardline groups had pledged to station monitors at polling booths.
More than 60,000 military and police have been deployed across the city to ensure voting runs smoothly.
All in all, there are pressures on the nominal Muslim (as well as on the non-Muslim) in this election.
The conciliatory tone contrasted with the fractious nature of a campaign that challenged Indonesia's religious and ethnically tolerant traditions, and comments made by Anies on the eve of the election.
"Arguably, the electorate wasn't so much impressed by his programme than by his presenting a compelling anti-Ahok persona". This explains why some find him arrogant. Ahok is different from the "common Indonesian political leader" because he does not refrain from taking certain decisions that benefit the community at large but are very painful for a limited number of locals.
Throughout the campaign Ahok has been the target of hardline Islamic groups who launched large-scale protests against him and urged supporters not to vote for a non-Muslim.
While he says there is no evidence the broader population has become more conservative, "the segment of militant Islamists is becoming more assertive" and their influence on elite processes, like elections, is increasing.
Incumbent governor Basuki 'Ahok' Tjahaja Purnama holds up his ballot before casting his vote in the Jakarta governor election in North Jakarta, Indonesia April 19, 2017.
The trial centres on comments that Purnama made a year ago about his opponents' use of the Islamic holy book in political campaigning. President Widodo and Ahok are allies.
He was catapulted to national prominence after becoming governor of Jakarta, with Ahok serving as his deputy.
The 47-year-old Baswedan supported President Joko Widodo's agenda, accelerating economic growth with higher assistance for small and medium business. This changed after the Golkar party selected a new leader, one who was not attached to Prabowo.
Baswedan was Widodo's campaign manager in the 2014 presidential election, when he beat Subianto.
Baswedan, who is Muslim, will take over as governor in October.
Last year, Ahok was seen as the strongest contender for the gubernatorial election in the country's capital.
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