Supporters of the ousted far-right leader also stormed the Supreme Court and surrounded the presidential palace.
But police regained control of the buildings in the capital Brasilia on Sunday evening after hours of clashes.
Brasilia’s Civil Police said 300 people have been arrested and officials have vowed to track down others involved.
The justice minister, Flavio Dino, has said the government is seeking information on “terrorist attacks”.
On Monday morning, heavily armed officers in the city gathered outside a camp of Mr Bolsonaro’s supporters – one of a number that have been set up outside army barracks around the country since October’s election.
Meanwhile, Brasilia’s governor, Ibaneis Rocha, has been removed from his post for 90 days by the Supreme Court.
Justice Alexandre de Moraes accused him of failing to prevent the riot and of being “painfully silent” in the face of the attack. Mr Rocha has apologised for Sunday’s events.
Pro-democracy rallies are being called by leftist leaders and groups across Brazil.
The dramatic scenes – which saw thousands of protesters clad in yellow Brazil football shirts and flags overrun police and ransack the heart of the Brazilian state – come just a week after Lula’s inauguration.
He toured the Supreme Court building on Sunday night to see the damage for himself.
The veteran left-wing leader was forced to declare emergency powers before dispatching the national guard into the capital to restore order.
He also ordered the closure of the centre of the capital – including the main avenue where governmental buildings are – for 24 hours.
Mr Dino said some 40 buses which had been used to transport protesters to the capital had been seized and he called the invasion an “absurd attempt to impose [the protesters’] will by force”.
Mr Bolsonaro has repeatedly refused to accept that he lost October’s election and last week left the country instead of taking part in inaugural ceremonies, which would have seen him hand over the iconic presidential sash.
The 67-year-old – who is believed to be in Florida – condemned the attack and denied responsibility for encouraging the rioters in a post on Twitter some six hours after violence broke out.
Speaking before he arrived in Brasilia, Lula said there was “no precedent in the history of our country” for the scenes in Brasilia and called the violence the “acts of vandals and fascists”.
And he took aim at security forces whom he accused of “incompetence, bad faith or malice” for failing to stop demonstrators accessing Congress. (BBC News)
