The latest arrests came as heavily armed police broke down pro-Bolsonaro encampments outside the army headquarters on Monday.
The rioting came a week after new president, Luiz Inácio Lula da Silva, known as Lula, was sworn in. Mr Bolsonaro, who lost last year’s election, has refused to concede defeat.
According to reports, he was admitted to a hospital in Florida on Monday, suffering from “abdominal pain”.
The rioters had been demanding that Lula was ousted and that Bolsonaro was given the presidency, despite his failing to win a second term in October’s general election.
Thousands of protesters wearing yellow Brazil football shirts and flags had managed to overrun police and lay siege to government buildings, forcing the president to declare emergency powers.
Rioters broke windows, toppled furniture, and destroyed works of art in state buildings.
They overturned the U-shaped table at which Supreme Court justices convene, ripped a door off one justice’s office and vandalised an iconic statue outside the court, leaving the building’s interior in ruins.
All of the buildings have now been retaken by security forces, according to local media.
However, elsewhere in the country, there are still people still trying to block roads and access to refineries, according to reports.
Government ministers said police have begun tracking those who paid for buses to bring rioters to the capital Brasilia and that buildings would be inspected for evidence to catch those responsible.
Justice Minister Flávio Dino said at a news conference: “They will not succeed in destroying Brazilian democracy. We need to say that fully, with all firmness and conviction.
“We will not accept the path of criminality to carry out political fights in Brazil. A criminal is treated like a criminal."
Monday’s arrests came in addition to 300 held on Sunday.