Ahok, an ethnic Chinese Christian, has been accused of insulting Islam after he quoted a verse from the Quran in a November speech.
Hardline Islamists say he shouldn't administer a Muslim-majority city.
After a panel of 5 judges read out the charges, Ahok told the court that what he said "was not intended to interpret the (Koran), moreover to insult Islam or the ulema."
An edited version of his speech went viral in November, provoking mass protests
by Indonesia's Muslim majority.
Ahok struggled to hold back tears while reading out his statement to the court, denying the charges and describing how he'd been raised by an adoptive Muslim family.
"My father and my adoptive father, vowed to be brothers until the end. The love of my adoptive parents for me, has inspired me to this day," he said.
Protestors duel with supporters
Outside the court, a few hundred anti-Ahok protesters yelled, "Jail Ahok, Jail Ahok!" Many are members of conservative Islamic groups, who want to see him behind bars.
One of the speakers, on a megaphone, blasted Ahok for his tearful statement, to a jeering crowd. "He said he didn't insult Islam. He was even crying."
Nearby a smaller group of the governor's supporters chanted, "Free Ahok, Free Ahok!"
The two sides were separated by a couple of armored police trucks and a cordon of unarmed police personnel.
Many of Ahok's supporters were his campaign volunteers, who've helped him in his re-election bid. Jakarta is scheduled to have an election for mayor on 15 February 2017.
A few of them shed tears too, as the court session went on.
"We want him freed. We are here to give him moral support," Cepu Suprianto said.
Asked if Ahok will get a fair trial, Suprianto said: "We can't intervene and we'll have to follow the legal process."
Ahok conviction likely: expert
Research fellow at the East Asia Program in Sydney's Lowy Institute, Aaron Connelly, told CNN the Ahok trial was a symbol of Indonesia's increasing conservatism.
"Blasphemy is a serious crime -- the unusual thing about this case is that it's very clear now that Ahok did not commit blasphemy ... it was misportrayed in the video that was put online and transcribed as Ahok saying that the Quran was wrong," he said.
But despite the misleading video, Connelly said he now believed Ahok was "more likely than not" to be convicted, if only due to political pressure.
"If Ahok is not found guilty, in fact, I'd be concerned about sectarian violence ... that if nothing else will lead the judiciary to convict him," he said.
Connelly said if Ahok was convicted and jailed, whoever took his place as Jakarta mayor would be well placed to challenge Ahok's former ally, President Joko Widodo, in the 2019 Indonesian Presidential election.
The next court date has been set for December 20.