Sao Paulo and defending champion River Plate advanced to the last 16, where the teams will face Toluca and Independiente del Valle respectively.
A 1-1 draw was enough for Sao Paulo to progress to the round of 16 in the Copa Libertadores ahead of The Strongest.
Only a point separated second-placed Sao Paulo and The Strongest heading into Thursday's sixth and final Group 1 fixture.
And Sao Paulo beat The Strongest to a spot in the knockout stages thanks to the stalemate in La Paz, Bolivia.
The Strongest made a dream start in front of their home fans at Estadio Hernando Siles, when Paraguayan midfielder Ernesto Cristaldo headed home a 29th-minute free kick from inside the six-yard box.