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Flamengo will meet River Plate in the final after crushing Gremio on Wednesday.
Gremio's hopes of reaching the final remain alive thanks to Pepe's late equaliser against Flamengo on Wednesday.
Everton and Alisson scored in the first half to level the quarter-final tie 2-2 on aggregate as Gremio progressed on away goals.
Palmeiras edged Gremio away from home to take control of their Copa Libertadores quarter-final.
A first-half brace from Andre led the way for Gremio, who set up an all-Brazilian quarter-final against Palmeiras on Thursday.
In the match between Gremio and Internacional in the Brasileirao, there was a awful incident to report. A woman, who was with her son, took her shirt off to celebrate the Gremio equaliser and various Internacional fans snatched it off her.
Everton opened the door for a move to Manchester United after scoring a late stunner in Brazil's 3-0 win over Bolivia in the Copa America.
Gremio are still clinging onto hope after no host venue for the second leg of the final was announced, pending the result of their appeal against the semi-final result.
Gonzalo Martinez's stoppage-time penalty saw River Plate past Gremio and into the Copa Libertadores final.