Atletico lost 1-0 to Atlético Nacional in the first leg of their last 16 tie in Medellin on Wednesday.
Autuori, who led Cruzeiro and Sao Paulo to Libertadores Cup glory, was blamed for the defeat, just his third in 23 games in charge of the club.
His replacement is Levir Culpi, an experienced former coach with Botafogo, Cruzeiro, Palmeiras and Sao Paulo, the club announced on Their web site.
Culpi signed a contract until the end of the year for what will be his fourth stint at the Belo Horizonte side.
He will meet the players at a training session on Friday and lead the team against Gremio in their second Brazilian Serie A game on Sunday.
Atletico drew last weekend's opener at home to Corinthians.