Bolsonaro's victory caps ones of the most polarizing and violent political campaigns in Brazil's history, amid a prolonged recession, rising crime rates and widespread corruption scandals.
In a victory speech Sunday, Bolsonaro said he was a "defender of freedom" who would run a government that protected citizens who "follow their duties and respect the laws."
"The laws are for everyone, this is how it will be during our constitutional and democratic government," he said.
Bolsonaro was declared the winner by the Supreme Electoral Tribunal after 94% of the votes were counted, easily defeating his leftist ex-Sao Paulo mayor Fernando Haddad.
The electoral tribunal released early results showing Bolsonaro leading with 55.54% of votes to Haddad's 44.46%, a difference larger than the amount of votes left to be counted.
But while Bolsonaro's supporters were rejoicing on Sunday, opponents voiced concerns that his victory could threaten human rights and ecological preservation in the world's fourth largest democracy.
Speaking earlier in the day, Haddad said Brazil's democracy was "at stake" in Sunday's vote. "I believe today is a great day for the country which has arrived at a crossroads," he said.