For the former army captain, the New Year's Day inauguration was the culmination of a journey from a marginalised and even ridiculed congressmen to a leader who many Brazilians hope can combat endemic corruption.
Tuesday's festivities in the capital Brasilia began with a motorcade procession along the main road leading to Congress and other government buildings.
Mr Bolsonaro and his wife, Michelle, stood up in an open-top Rolls-Royce and waved to thousands of onlookers.
They were surrounded by dozens of guards on horses and plain-clothes bodyguards who ran beside the car.
Once inside Congress, Mr Bolsonaro and his vice president, retired Gen Hamilton Mourao, took the oath of office.
Mr Bolsonaro then read a short speech that included many of the far-right positions he staked out during the campaign.
He promised to combat the "ideology of gender" teaching in schools, "respect our Judeo-Christian tradition" and "prepare children for the job market, not political militancy".
"I call on all congressmen to help me rescue Brazil from corruption, criminality and ideological submission," he said.
A fan of US President Donald Trump, the 63-year-old long-time congressman rose to power on an anti-corruption and pro-gun agenda that has energised conservatives and hard-right supporters after four consecutive presidential election wins by the left-leaning Workers' Party.
Mr Bolsonaro was the latest of several far-right leaders around the globe who have come to power by riding waves of anger at the establishment and promising to ditch the status quo.
"Congratulations to President @jairbolsonaro who just made a great inauguration speech," Trump tweeted. "The USA is with you!"
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