Friday's demonstration started peacefully but descended into chaos as night fell with protesters torching police cars and hurling rocks and bottles in the heart of Jakarta, as they demanded the leader be jailed for blasphemy.
Scores of police officers were injured and one man died in the clashes close to the presidential palace, reportedly after tear gas fired by authorities triggered an asthma attack.
The protest involving tens of thousands of hardliners was sparked by accusations governor Basuki Tjahaja Purnama, a Christian and a member of Indonesia's ethnic Chinese minority, insulted the Koran while campaigning in elections for the Jakarta governorship.
Police had already launched the investigation into Purnama, known by his nickname Ahok, before Friday's protest after Muslim groups accused him of breaking the country's tough blasphemy laws.
The governor was questioned as a witness at national police headquarters in Jakarta, emerging after nine hours and making his way through a media scrum.
Purnama dodged questions about the case, only telling reporters: "I want to go home, I'm hungry."
Police said they plan to finish questioning about 30 witnesses over the case this week and will decide next week whether any crime had been committed.
Purnama has apologised for his remarks, claiming that he was criticising his political rivals who were using the verse rather than the Koran itself. But this has done little to appease his opponents.
Thousands of police and soldiers were deployed before the rally in the capital of the world's most populous Muslim-majority nation, but it still took officers hours to quell the violence with tear gas and water cannons.
The protest also forced President Joko Widodo to cancel an official visit to Australia due to start at the weekend.
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