The incumbent governor of Jakarta, Basuki "Ahok" Tjahaja Purnama, an ethnic Chinese Christian, is facing a challenge by a Muslim former government minister backed by hard-line religious groups.
Groups determined to see Baswedan take the governorship have been accused of stoking religious discord in the city ahead of the second round, analysts say, a startling turn in a country with a secular constitution and a long tradition of pluralism.
"I think a lot of Chinese Jakartans are feeling anxious about what will happen regardless of the outcome," Ian Wilson, research fellow at Australia's Murdoch University Asia Research Center, told CNN.
Official results won't be known for about two weeks but a number of quick counts will begin after voting closes at 1 p.m. local time.
Mass protests against Ahok
Tensions began to build in November 2016 after Ahok made comments during a campaign speech, which were interpreted by some as an insult to the Quran and Islam.
Now Ahok is on trial for blasphemy and Islamic conservative groups are pushing hard against him. In March, during the campaign, large crowds of thousands of protestors massed in Jakarta's streets to call for his imprisonment.
"(The vote) is being framed in these semi-apocalyptic terms -- that if Baswedan loses it means this infidel, conspiratorial Chinese group will be in power and it will be a disaster," Wilson said.
While Baswedan himself has taken a step back from the aggressive rhetoric of the first half of the campaign, analysts say, conservative Islamic groups have picked up the slack.
"There was this grandma who died and she voted for Ahok and she was (reportedly) denied Muslim funeral rights," Tobias Basuki, a researcher at the Center for Strategic and International Studies, an Indonesian think tank, told CNN.
"(Islamist groups) are using a lot of very blatant religious messages. Very blatant. There are various messages showing people ... making oaths in communities saying you cannot vote for a non-Muslim and so on."
With polls showing a tight race between the two candidates and religious tensions running high, both camps have reasons to be anxious.
Wilson said there is a possibility things may descend into violence.
Anies for president?
It isn't just religious tolerance that's at stake though.
The eyes of Indonesia's national leaders are fixed on the vote as well, and who will be in the powerful position of Jakarta governor during the next national election in 2019.
Ahok is an ally of Indonesian President Joko Widodo, also known as Jokowi -- in fact, he was his running mate during Widodo's own successful run for the governorship in 2012.
After Widodo's 2012 win quickly led to a successful run for the presidency in 2014, Indonesian political insiders now see the Jakarta governorship as a step to the highest office in the land.
A Baswedan win will be seen as a major blow to Jokowi.
"It would be a major political win for (former 2014 presidential candidate) Prabowo Subianto, who has been very transparent in his support for Anies," Wilson said.
Whether Baswedan runs for the presidency in 2019, or supports a second run by Prabowo, Basuki said a win by the former minister in Jakarta would embolden Islamic groups.
"If Anies (is elected), the peddling of influence by these Islamic groups will be greater, and use of religion will be much more in vogue in local elections heading towards the 2019 vote," he said.
Jakarta's poor turn on Ahok
But despite the high religious and racial tensions in the Jakarta governor race, they aren't the only reason Ahok is in trouble.
Greg Fealy, an associate professor in Australian National University's Coral Bell School of Asia Pacific Affairs, told CNN in February Ahok's blunt, combative style of governing put a lot of Jakartans off.
"He's a very combative, outspoken, reckless kind of character who has achieved a lot for Jakarta, but he's a character who has created a lot of antipathy toward him," he said.
Not only that, but a lot of the poor Jakartans who voted for the joint Widodo/Ahok ticket in 2012 in hopes of a new style of government have been the target of large-scale evictions under the governor's administration.
"They have very specific material grievances against the governor, they feel there was a betrayal of a political contract ... I think that magnified feelings of injustice against those neighborhoods," Wilson said.