Autuori will be replaced by Levir Culpi, who was with Cerezo Osaka until last year.
Thursday's decision to fire Autuori came a day after Atletico Mineiro lost 1-0 to Atletico Nacional of Colombia in the first leg of the round of 16 of the Copa Libertadores.
Fans had been calling for Autuori's dismissal because of the team's poor play and disappointing results this year. Atletico won 11 matches and lost three since he took command after the Club World Cup in December 2013.
Autuori had previously coached Peru and Qatar, as well as other Brazilian clubs.
This will be Culpi's fourth stint with Atletico. The last time was in 2007, before he moved to Japan.
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