"José Mauro Coelho submitted his resignation this morning (Monday)," Petrobras said in a statement.
A few hours later, the largest company in Latin America announced that Fernando Borges, director of the exploration and production department, had been named interim president.
Mr Coelho was sacked a month ago after just 40 days in office.
But he remained in office while waiting to be formally dismissed at the company's next shareholders' meeting, where the Brazilian state has the majority.
This assembly should take place in July.
Petrobras announced Friday an increase of 5.18% in the price of gasoline and 14.26% of diesel.
In the aftermath, President Bolsonaro accused the CEO of "betraying the Brazilian people" and threatening to "plunge the country into chaos".
He also called for the opening of a parliamentary commission of inquiry against the leaders of Petrobras.
After the announcement of Mr. Coelho's resignation, trading in Petrobras shares was "temporarily suspended" during the morning.
After the resumption, around 11:00 a.m. (4:00 p.m. GMT), they were down slightly (0.5%) at midday.
On Friday, the company's ordinary shares fell 7.25% and preferred shares 6.09%, after falling more than 10% during the session.
Jair Bolsonaro, who is trying in vain to change the company's pricing policy, linked to the international market, had already dismissed two other Petrobras bosses since the start of his term in January 2019.
© 2022 AFP