The unrest on Thursday forced the legislature to delay a vote on controversial changes to election laws that could further enhance the political influence of outgoing President Joko Widodo.
Parliament met in an emergency session to overturn one decision made by the Constitutional Court on election procedures, while amending another.
Protesters occupied roads in front of the parliament building in Jakarta. Some held banners and signs, while others started a fire and burned tires.
The Constitutional Court on Tuesday dismissed a challenge to an age limit that prevents people under 30 running for regional governorships, which would prevent Widodo's youngest son, Kaesang Pangarep, 29, running in a regional contest in Central Java.
Protesters tore down a section of fence and threw stones at police outside parliament in Jakarta. (AP PHOTO)
The court also made it easier for political parties to nominate candidates by cutting back a requirement that they hold 20 per cent of a local legislature.
Parliament on Wednesday passed an emergency motion to change the minimum age to serve as governor to 30 at the time of inauguration and further ease nomination requirements, and planned to ratify the vote in a plenary session on Thursday.
The moves triggered widespread condemnation on social media and raised concerns about a potential constitutional crisis.
The legislature was forced to delay passing the law after failing to achieve a quorum.
Widodo's eldest son, Gibran Rakabuming Raka, is the incoming vice-president after the same court created an exception to the age limit for the post for former regional leaders.
The decision was made while Widodo's brother-in-law, Anwar Usman, was serving as chief justice.
Protesters fears the law changes could further enhance the influence of outgoing President Widodo. (AP PHOTO)
Usman was criticised for taking part in a case involving a close relative and later dismissed.
Activists, students, workers and Indonesian celebrities and musicians also joined the protest on Thursday, voicing concerns about democracy in Indonesia.
Protests were also reported in other big cities, including Bandung, Yogyakarta, Surabaya and Makassar.
In Yogyakarta, at least 1000 protesters rallied in front of Yogyakarta's parliament building, the state palace and the city's ceremonial centre.
Their demands included voting down the regional election bill, respecting the Constitutional Court's ruling and rejecting political dynasties.
The simultaneous protests in major cities showed anger at parliament's efforts to overrule the Constitutional Court decision to allow more candidates to compete in the regional elections, said Yoes Kenawas, a political analyst at Atma Jaya Catholic University.
"They also opposed the dynastic politics carried out by President Jokowi," Kenawas said.
