Brazil’s new president Luiz Inacio Lula da Silva who took office on January 1 after defeating Mr Bolsonaro in the October vote, promised to bring those responsible for the violence to justice.
The mobs rampaged through Congress, the Supreme Court and presidential offices, smashing windows, furniture and artwork.
Mr Bolsonaro went to a hospital in Orlando 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 has an intestinal blockage that was not serious and would likely not need surgery.
Mr Bolsonaro faces several investigations before the Supreme Court in Brazil and his future in the United States, where he traveled with a visa issued to heads of state, diplomats and other government officials, is in question.
Representative Joaquin Castro, a Democratic lawmaker in the US Congress, said on CNN that the United States should not give refuge to an “authoritarian who has inspired domestic terrorism” and should send Mr Bolsonaro back to Brazil.
The US government declined to comment on Mr Bolsonaro's visa.
US State Department spokesperson Ned Price said a person who entered on a visa for foreign officials must depart the country within 30 days or apply for a change of immigration status if they are no longer engaged in official business.
Brazilian soldiers backed by police on Monday dismantled a camp opposite the army's headquarters where Bolsonaro supporters have been protesting since he lost the election, restoring order in the Brazilian capital.
Thousands of Bolsonaro's backers set off marching from that encampment on Sunday before storming the presidential palace, Supreme Court and Congress in the worst attack on state institutions since Brazil's return to democracy in the 1980s.
Riot police on Monday cleared the two-month-old camp, according to Reuters witnesses, while detaining roughly 1,000 people for questioning.
Lula, who was back at work at the ransacked Planalto palace, met with his defense minister and commanders of the armed forces to discuss the violence reminiscent of the assault on the U.S. Capitol two years ago by backers of former President Donald Trump.
US president Joe Biden joined other world leaders in condemning Sunday's riots, calling them “outrageous,” while Bolsonaro, who is now in Florida, denied inciting his supporters and said the rioters had “crossed the line”.
Pro-Bolsonaro truckers, who have caused intermittent havoc on Brazil's highways for months, held more protests through Sunday night, blocking the BR 163 highway that cuts through Brazil's top grain-producing state Mato Grosso. Police said blockages on another highway in Parana state were also cleared.
“There are still people trying to block roads and access to oil refineries," presidential spokesman Paulo Pimenta told reporters. State-run oil company Petrobras said its refinery operations and fuel supplies had not been affected.
Supreme Court Justice Alexandre de Moraes ordered the governor of Brasilia removed from office late on Sunday for 90 days over alleged security failings and demanded that social media platforms Facebook, Twitter and TikTok block accounts of users spreading anti-democratic propaganda.
Facebook parent Meta said on Monday it was removing content supporting or praising the weekend actions. Telegram, TikTok, Twitter and YouTube did not immediately respond to requests for comment.
Brazil's financial markets held steady after an early drop, with the Bovespa benchmark stock index edging higher in afternoon trading and the currency closing 0.4 per cent weaker against the U.S. dollar. Some analysts said Sunday's violence could strengthen Mr Lula politically.