It was a day of upsets as Atletico Mineiro and Palmeiras failed to qualify for the Copa Libertadores quarter-finals, while Gremio advanced.
Mineiro played out a goalless draw against Wilstermann in Belo Horizonte on Wednesday but crashed out 1-0 on aggregate.
Trailing the Bolivians 1-0 following last month's first leg, 2013 champions Mineiro tried to erase the deficit but Robinho's men were unsuccessful at Estadio Governador Magalhaes Pinto.
Wilstermann will face Argentina's River Plate in the last eight, scheduled for next month.
Fellow Brazilian side Palmeiras suffered the same fate in the last 16, albeit 5-4 on penalties against Barcelona.
Palmeiras triumphed 1-0 in the second leg thanks to substitute Moises' 51st-minute strike.
A swift counter-attack saw Moises fire the ball into the top corner of the net to level the tie 1-1 on aggregate against their Ecuadorian opponents.
But the 1999 champions came unstuck in the shoot-out after Egidio missed his penalty.
Barcelona will play either Atletico Paranaense or Santos in the next round.
Pedro Rocha scored twice as Gremio came from behind to beat Godoy Cruz 2-1 on Wednesday and 3-1 on aggregate.
Nacional or Botafogo await Gremio for a spot in the semi-finals.