But the 80-year-old, who took just under 52% in the run-off vote, now faces a hostile Congress and divided country.
The winner: Brazil's left-wing President Luiz Inácio Lula da Silva has won a fourth term in office, defeating his right-wing challenger Flávio Bolsonaro.
Lula won 51.79% of the vote, while Bolsonaro had 48.21% - that's a difference of more than 4 million votes. It's also a historic bounce back after Lula lost the first round of voting.
Flávio Bolsonaro has not taken the loss lightly, he's called for the result to be annulled and said it was "impossible to recognise". For his supporters, it's been a devastating blow.
Lula's victory was far from certain: Lula was in second place at 45% during the first round on 4 October, while Bolsonaro was ahead at 47%. Lula went from second to first place in 211 municipalities between the two rounds.
There's been no word yet from US President Donald Trump after he said he would be watching the elections. Our Global affairs reporter Mimi Swaby explains that Bolsonaro had US backing
Bolsonaro - who won the first round - says the result is "inexplicable" and calls for it to be annulled, a supporter says he was "more than upset". Our Latin America editor explains what's happening
His father, ex-president Jair Bolsonaro, is currently serving a jail sentence under house arrest for plotting a coup after losing the last election
Things felt tense in the capital, after the results came in and Flavio Bolsonaro rejected the result, says our correspondent in Brasilia
Brazilians went to the polls and gave Flavio Bolsonaro a first-round lead of 2.2 million votes over Luiz Inácio Lula da Silva.
But three weeks later, Lula won the presidency by a margin of four million votes. The scale of the turnaround was remarkable. Between the two rounds, Lula gained around 11 million additional votes.
So, how did he do it? Three factors help explain:
First, turnout increased. More than 2.3 million additional voters cast ballots in the second round compared with the first
Second, Lula appears to have won over many voters who either abstained or declined to back a candidate in the first round. The number of blank and spoilt ballots fell by about 1.8 million
Third, he succeeded in persuading some voters who had previously backed Flavio Bolsonaro or other candidates to switch sides
Things felt tense here in the capital, Brasilia, after the results came in and Flavio Bolsonaro rejected the result.
There are concerns about whether this could trigger unrest with his supporters. Many remember the scenes of his father Jair Bolsonaro’s supporters storming government buildings and the Supreme Court here ahead of Lula’s 2023 inauguration after they did not recognise the last election result.
So far, things are calm here.
And there are a few differences to 2022's result that suggest it would be harder to try something similar.
Firstly, I remember covering Bolsonaro senior's coup trial here last year and it was striking how much the evidence revealed about how he tried to use the machinery of the state – and senior figures within it – as president, to cling on to power. Because President Lula is the incumbent this time, Flavio Bolsonaro can't try that.
Secondly, this result was not as close as 2022, so it would be a lot harder to claim irregularities.
While Bolsonaro shares a lot of his father's traits, he has framed himself as the more "moderate" Bolsonaro, the "vaccinated" one even – so would he really go there? He has seen the consequences such rhetoric and actions had for his father.