Basuki Tjahaja Purnama, also known as Ahok, has faced demonstrations
calling for his ouster amid allegations of blasphemy.
An ethnic Chinese Christian, Ahok is currently under investigation by Indonesian police
over a speech he gave in which hardline Islamists claim he insulted the Quran.
Police estimate around 200,000 people converged on Jakarta's main square Friday for noon prayers.
Islamist groups, NGOs, students and ordinary citizens came from Jakarta and other cities and towns outside the capital.
Protesters chanted "jail Ahok," and called for him to be detained while the blasphemy case is ongoing.
"It's not about ethnicity or religion," a protester called Agus told CNN. "It's only this one person who needs to be brought to trial."
"It's a matter of what he has done," he said.
Supporters of Ahok gathered Friday outside his headquarters to pray for him, according to a statement from the campaign team.
The accusations of blasphemy surround Ahok's quoting of a Quranic verse in a stump speech.
He is currently standing for re-election as governor, and has faced attacks on his Christian faith, with some opponents claiming that Muslims were forbidden by the Quran to vote for him.
In a speech last month, Ahok quoted a verse from the Muslim holy book and said that people had been "lied to" by those saying they would go to hell for voting for him. There was widespread outrage after an edited video of his speech went viral.
Speaking at Friday's protests, Suci, a volunteer at an Islamic NGO, said that if a Muslim is standing for election "we have to choose (the) Muslim."
Noor Huda Ismail, founder of the Institute for International Peace Building in Indonesia, told CNN last month that Ahok, a key ally of Indonesian President Joko Widodo, is an easy target for the enemies of the President, who's popularly known as Jokowi.
"He's a stepping stone (to Jokowi). You see people no longer talking about the blasphemy case but about wanting to topple the government," Ismail said.