Jakarta police spokesman Awi Setiyono said an elderly man died, possibly from the effects of tear gas. He said four civilians and three police officers were injured.
Clashes broke out between police and hard-core protesters who refused to disperse following nightfall. Police fired tear gas and water cannons and protesters set alight two police vehicles and piles of rubbish left behind from the protest, which drew tens of thousands of people.
The confrontation subsided after a protest leader appealed for calm.
MetroTV reported that a mob tried to enter the housing complex where Jakarta Gov. Basuki "Ahok" Tjahaja Purnama lives in northern Jakarta but were stopped by police, who fired tear gas.
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Setiyono said rioting in north Jakarta involving the looting of a convenience store and damage to police vehicles had been brought under control.
President Joko "Jokowi" Widodo planned to hold an emergency meeting with Cabinet ministers and top military and intelligence officials, according to MetroTV.
The predominantly male demonstrators, most wearing white shirts and skull caps, had massed at the Istiqlal Mosque for the protest following weekly Friday prayers and marched on the nearby presidential palace.
Large protests also took place in other cities including Medan on Sumatra, Makassar in Sulawesi and Malang in East Java.
Members of an Islamic student group threw plastic water bottles and other objects at riot police in Jakarta, but the massive demonstration appeared to have gone off without any major incident during the day.