Brazil president Mr Da Silva supported the anti-amnesty protest
With the voting, Mr Bolsonaro could only be able to run for president in 2030.
German Chancellor Olaf Scholz is set to travel to Brazil on Monday to meet new President Luiz Inácio Lula da Silva.
Six of those 46 hospitalised in Brasilia are in serious condition and two required emergency medical care.
Mr Bolsonaro was already under investigation in four Supreme Court criminal probes before stepping down as president.
Incumbent president Jair Bolsonaro lost the presidential contest to the leftist government of Luiz Inácio Lula da Silva.
Mr Bolsonaro’s right-wing Liberal Party won 99 seats in the 513-member lower house, up from 77, and right-leaning parties allied with him now control half the chamber.
Voting is compulsory in Brazil and more than 156 million people are eligible to vote in today’s presidential election.
Almost nothing is known about how doctors working as first responders are keeping safe from COVID-19.
