Cruzeiro - leaders of the Brazilian Serie A - edged out Santos 1-0 in the opening leg of their semi-final but league form was not a clear indication in Rio de Janeiro with hosts Flamengo upsetting Mineiro at the Maracana.
Flamengo entered the match eight positions adrift of Mineiro in the league standings but overcame their in-form rivals with two goals in the final half hour.
Mineiro were on a six-game unbeaten run but had no answer to the home team late in Wednesday's first leg with Victor Caceres and Chicao getting the goals for Flamengo.
Caceres made it 1-0 in the 61st minute, heading Gabriel's cross home after Flamengo's initial free-kick had looped from one side of the penalty area to the other, while Chicao doubled the hosts' lead from the spot with 11 minutes remaining.
Mineiro's Josue inexplicably attempted to take the ball off Gabriel's toe by diving head first but only managed to barge into the legs of the Flamengo striker.
In Belo Horizonte, Willian struck the winner for Cruzeiro in the 11th minute, following up his own blocked shot to curl the ball inside the far post.