There were also fears he would implement Islamic sharia regulations in the Indonesian capital, which he denied.
Despite enjoying a high satisfaction rate for his performance in office as governor, Ahok receieved only 42% of the vote to his Muslim opponent and former education minister Baswedan's 58%.
Tensions have eased Wednesday night in Jakarta after the election, said Wilson, the Murdoch University research fellow.
(AP Photo/Tatan Syuflana). Indonesians queue up give their votes at a makeshift polling station under a bridge during the runoff election in Jakarta, Indonesia, Wednesday, April 19, 2017. Residents of the Indonesian capital are electing a governor afte.
Baswedan will officially take over as governor in October.
Official results are not expected until early May but the private pollsters, who count a sample of votes, are usually accurate.
Mr Anies, a scholar who many viewed as moderate, drew criticism during the campaign when he aggressively courted the conservative Islamic vote. Mass rallies held by Islamist activists have called into question Indonesia's reputation as a home to a more moderate form of Islam.
It came a day before Vice President Mike Pence was scheduled to visit Indonesia and meet with Widodo on the third leg of an Asian Pacific tour that includes South Korea, Japan and Australia.More news: 'The Sword Stands Ready': Mike Pence Issues Pointed Warning to North Korea
"Going forward, we want everyone to forget the tensions during the campaign period and election". Baswedan told reporters that he is committed to maintaining the diversity of Jakarta and will emphasize social justice.
Purnama, who was initially the clear favorite to win, is now standing trial due to his remarks, in which he criticized people who cited a verse from the Quran to discourage Muslims from voting for him.
Airlangga is a member of Ahok's Golkar Party and a member of President Joko "Jokowi" Widodo's Cabinet, making him a natural ally of the sitting governor who lost yesterday's gubernatorial poll.
If convicted, he faces a maximum five-year jail sentence, though could still govern while appeals are heard.
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.
In the west Jakarta neighborhood of Kebon Jeruk, Annisa Karolina, a 29-year-old restaurant cashier, said voting for a non-Muslim would be a sin, but she also believes Jakarta will be better run without Ahok.
Jakarta's police chief Mochamad Iriawan confirmed a number of people were taken into custody for their conduct at some polling booths in the city. Or how much did it play into the fact that this was a Christian and that radical Muslims within Indonesia are saying, 'We shouldn't have a Christian in this leadership role.
Police said 15 people were detained following disturbances at polling stations in the city of 10 million people, after what the Jakarta Post dubbed "the dirtiest, most polarising and most divisive" election campaign the nation had ever seen.