Thousands of Bolsonaro supporters stormed the seats of power in Brasilia and ransacked the Supreme Court, Congress and presidential offices - following the election of leftist President Luiz Inacio Lula da Silva, known as Lula.
Police finally regained control of the buildings in the capital Brasilia after hours of clashes, and more than 1,500 people were detained.
Police are said to have five days in which to charge suspects once they have been arrested.
Lula, who took office on January 1 after defeating Mr Bolsonaro in the October vote, promised to bring those responsible for Sunday’s violence to justice.
Meanwhile Brazil’s 11-day-old government on Wednesday braced for more anti-democratic protests by far-right former president Bolsonaro’s supporters, whose rampage through government on Sunday threatened the country’s political stability.
Lula’s government bolstered security measures nationwide as flyers appeared on pro-Bolsonaro social media calling for mass demonstrations in Brazilian cities to “retake power.”
“We have measures for this Wednesday to reinforce security throughout the country since pamphlets of new demonstrations have been circulated,” Lula’s chief of staff Rui Costa said late on Tuesday after a cabinet meeting.
Faced with the threat of new protests, the government’s Solicitor General asked the Supreme Court to prohibit road blocks across Brazil and the invasion of public buildings.
His office also asked for a temporary ban on demonstrations and fines for companies found to be financing the logistics of the anti-democratic protests.
Authorities have sought to block Bolsonaro’s assets and arrest warrants were issued on Tuesday for officials responsible for public security in Brasilia for allowing Sunday’s insurrection - the worst assault on democracy since Brazil’s military dictatorship ended in 1985.
Meanwhile Bolsonaro, who left Brazil 48 hours before his term ended and has yet to concede defeat by Lula in the October elections, said on social media from Florida he planned to return to Brazil earlier than planned for medical reasons.
The former president was admitted to a hospital in Orlando, Florida, on Monday with intestinal pains related to a stabbing he suffered during the 2018 election campaign, his wife, Michelle, said on Instagram.
His doctor said he had an intestinal blockage that was not serious and would likely not need surgery.