Mr Bolsonaro won with 46.7 percent of the votes in a convincing first-round victory.
The win means the race will be sent to a runoff.
Mr Bolsonaro, who is a hard-line candidate running on an anti-socialist platform, has compared his campaign to US President Donald Trump’s 2016 run.
He is attempting to capitalise on a feeling of political disillusionment felt by the Brazilian people after the impeachment of successive presidents amid corruption allegations.
His fiery campaign hopes to galvanise the disenfranchised electorate.
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Mr Bolsonaro will face the left-wing Workers’ Party (PT) candidate, Fernando Haddad, in the second round on October 28.
A second round is required to determine a winner as Mr Bolsonaro did not win 50 percent of the votes needed to win outright.
With almost every vote counted, Mr Bolsonaro had 46 percent and Mr Haddad had 29 percent.
But the convincing victory is still not enough under the Brazilian system to swear in the far-right Mr Bolsonaro.
Mr Bolsonaro has used his campaign to court the evangelical Christian vote.
The far-right firebrand quoted the Bible as he cast his vote.
He said: “Our banner was always John 8:32: ‘Then you will know the truth, and the truth will set you free’.”
Mr Bolsonaro has attracted controversy with racist, homophobic and misogynist remarks and there have been mass-scale protests against him.
The populist front-runner declared he is “Brazil’s answer to Donald Trump”.
The 63-year-old, who is pro-torture, wants to focus on tacking crime and corruption.