Basuki Tjahaja Purnama, better known as "Ahok", is accused of insulting Islam during election campaigning.
Two protests against him, the last bringing together 200,000 conservative Muslims, have been held in the city.
Indonesia is the world's largest Muslim-majority nation.
Mr Purnama is Christian and ethnic Chinese - a double minority in Indonesia, where ethnic Chinese are about 1% of the population.
Sunday's counter-rally was pitched as a "parade of Indonesian culture".
It featured traditional dances from across the country and a giant flag proclaiming "We Are Indonesia". Police said 30,000 people attended the rally.
The Jakarta Post said the rally was organised by two parties that are part of President Joko Widodo's coalition. Mr Widodo is a political ally of Mr Purnama, but turned up for the last rally against him on Friday.
Speaking from the stage on Sunday, Surya Paloh, the chairman of the National Democratic Party, said Indonesians could not work together if they were "scattered, blaspheming, humiliating each other and no longer trust each other".
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In a campaign speech in September, Mr Purnama said Islamic groups who were using a Koranic verse to discourage support for him were deceiving voters. The verse is interpreted by some as prohibiting Muslims from living under the leadership of a non-Muslim.
Islamic groups said he had criticised the Koran and lodged complaints with the police.
Mr Purnama later apologised but denied committing blasphemy, which carries a maximum five-year jail sentence.
On Wednesday, Indonesian prosecutors confirmed his case could go to trial.
A large protest against the governor on 4 November turned violent, leaving one man dead and dozens of police and demonstrators injured. A larger rally was held on Friday.
Tens of thousands of people have turned out for what was billed as a unity rally in Indonesia's capital Jakarta, held to counter demonstrations against the city's governor.