Thursday's 1-1 draw away to Cerro Porteno was enough for River Plate to reach the semi-finals 3-1 on aggregate.
Gabigol scored to earn Flamengo a 1-1 draw away to Brazilian rivals Internacional and a 3-1 aggregate victory.
Everton and Alisson scored in the first half to level the quarter-final tie 2-2 on aggregate as Gremio progressed on away goals.
Ignacio Fernandez and Rafael Borre both scored penalties to lead River Plate past Cerro Porteno in Buenos Aires on Thursday.
Boca Juniors and Flamengo closed in on the last four in the Copa Libertadores.
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.
Boca Juniors were too good for Athletico Paranaense in the last 16 of the Copa Libertadores.
Franco Armani was the hero as River Plate edged Cruzeiro in the last 16 of the Copa Libertadores.
Goals from Diego Tardelli and David Braz helped Gremio beat Libertad in the Copa Libertadores.