The senator wrote on social media that his father had chosen him for "the mission of carrying on our project for the nation."
The head of Bolsonaro's right-wing Liberal Party, Valdemar Costa Neto, confirmed in a statement that the ex-president, who is serving time for a failed coup plot, had tapped his eldest son as the party's presidential candidate.
The news rattled Brazilian markets on Friday, with the country's currency slipping as much as three per cent against the US dollar and the benchmark stock index Bovespa down around four per cent.
The ex-president's endorsement on Friday underscored his eldest son's standing as the Bolsonaro family's most established politician in Brasilia.
Flavio Bolsonaro, 44, was elected to the Senate in the 2018 general election in which his father rode a right-wing groundswell of anti-establishment sentiment to the presidency.
The senator served previously as a state politician in Rio de Janeiro and mounted an unsuccessful run for Rio mayor in 2016, drawing 14 per cent of votes in the first round.
His brother Carlos Bolsonaro, 42, a Rio city councilman for over two decades, played a key role in his father's digital media strategy but has not ventured a run for higher office.
Younger brother Eduardo Bolsonaro, 41, a federal politician, is on trial for courting interference from Washington in his father's Supreme Court case after moving to the United States.
"Flavio unites the base, has good political dialogue and has my full support. He has all the qualities for this presidential race," the Brazilian congressman told Reuters.
Michelle Bolsonaro, 43, the ex-president's third wife, has so far tamped down speculation that she could make her first run for public office next year.
The former president has been barred from running for office since June 2023, when Brazil's federal electoral court condemned his conduct during the 2022 election.
In September, he was sentenced to 27 years and three months in prison for plotting a coup after losing the 2022 presidential election to Lula.
with AP