The increased security came at the request of the incoming president, who was stabbed in the stomach during a campaign rally in September.
But there has been no sign of him dropping the bluff, shoot-from-the-lip style that has earned him comparisons with US President Donald Trump, whom he admires. Bolsonaro then read a short speech that included numerous far-right positions he staked out during the campaign.
"We can not continue flirting with communism", Bolsonaro said following his victory. Military tanks, fighter jets and even anti-aircraft missiles also were deployed.
Journalists attending the inauguration complained about their treatment after they were required to arrive at the event seven hours early.
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There are also concerns for Brazil's extensive and diverse environment, with Bolsonaro's pro-business push being made at the expense of preservation - especially in the Amazon, sometimes called "the lungs of the planet" and at risk from increasing deforestation. Mr Bolsonaro, a nationalist who rails against globalisation, has pledged to follow the lead of the Trump administration by moving Brazil's embassy in Israel from Tel Aviv to Jerusalem. Bolsonaro, a vocal critic of media that voice opposition to him, has promised to cut advertising funds from state-owned companies to some media organizations.
"We are counting on Congress to provide the judicial support so police can do their jobs", Bolsonaro said, signaling that he may soon submit legislation that would allow police to be tried outside the criminal system.
Leftist Presidents Nicolas Maduro of Venezuela, Daniel Ortega of Nicaragua and Miguel Díaz-Canel of Cuba, deemed dictators by Bolsonaro, were uninvited by Bolsonaro's team after the foreign ministry sent them invitations.
In the audience were visiting delegations from 46 nations, including the U.S. secretary of state Mike Pompeo and the Israeli prime minister Binyamin Netanyahu.
While Bolsonaro enjoys sky-high approval ratings, many in Brazil fear his nostalgia for the military dictatorship that reigned from 1964 to 1985, his hardline approach to fighting crime and his record of disparaging women and minorities could herald a harsh shake-up.
"I will work tirelessly so that Brazil reaches its destiny", Bolsonaro added.