More than 80% of Indonesia's population professes Islam.
Political watchers such as Associate Professor Leonard Sebastian have said this election will be a litmus test of the strength of Indonesian pluralism underlined by its national ideology of Bhinneka Tunggal Ika, which means "unity in diversity".
Anies Baswedan had secured with around 58 per cent versus 42 per cent of the vote for Ahok, according to the quick counts.
Separating truth from fiction in this election has also been a challenge for the candidates with social media and instant messaging services like Whatsapp spreading lies and conspiracy theories.
One Twitter user, @fuadhn, said Indonesians "can feel what USA and British citizens feel now".
Southeast Asia's biggest economy grew 5.2 percent in 2016 and the government expects a repeat of that this year.
"(These) election campaigns. have been the dirtiest, most polarizing and most divisive the nation has ever seen, far worse than that for the 2014 Presidential election", the Jakarta Post editorial said Wednesday.
Prabowo Subianto, head of the Gerindra Party that Baswedan represents, said in a video message recorded over the weekend that "religious people need a leader who respects their beliefs".
More than 7.2 million people were registered to vote in the polls, which are also important as politicians view them as a potential stepping stone to the presidency in 2019.
Around 66,000 police and military personnel will be deployed on voting day, police spokesman Boy Rafli Amar said.
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The allegations drew hundreds of thousands of conservative Muslims onto the streets of Jakarta in major protests, and led to Purnama being put on trial for blasphemy in a case critics see as politically motivated.
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.
"Anies was largely the anti-Ahok candidate", Marcus Mietzner, an Indonesian politics expert at the Australian National University, said.
Despite Mr Purnama's first-round victory, former education minister Mr Baswedan, 47, was initially seen as the favourite in the run-off because the votes from a third, Muslim candidate who was knocked out were expected to go to him.
His platform has focused on improving public education, providing no-deposit home loans for low income groups and opposing a giant seawall in Jakarta Bay. Baswedan has denied he plans to implement Islamic sharia law in Jakarta if elected.
Baswedan will officially take over as governor in October.
Basuki congratulated his rival in a news conference.
Purnama stressed that he still has six months in office and promised to help Baswedan's transition. "We hope that in the future everyone can forget the campaign period".
Purnama was charged with blasphemy and is facing a maximum five-year jail term if found guilty.
Kartika Wirjoatmodjo, chief executive officer of the country's largest state bank, Bank Mandiri, said in an interview that whoever won "we (should) make sure it doesn't affect any of the long-term policies, especially on the openness and. ease of doing business and attracting investment".
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