Sao Paulo and defending champions River Plate advanced to the last 16, where they 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 the sixth and final Group 1 fixture.
And Sao Paulo pipped 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.
But Sao Paulo hit back on the stroke of half-time, Jonathan Calleri rising highest to direct a header past goalkeeper Daniel Vaca.
The match ended on a fiery note after Sao Paulo keeper Denis was sent off in stoppage time for a second yellow card as tempers erupted, with Calleri also seeing red.
River Plate advanced as group winners courtesy of their 4-3 victory over Trujillanos.
Former Argentina international Andres D'Alessandro - back at River for the first time since leaving for Europe in 2003 - scored a first-half brace to inspire the title holders in Buenos Aires.
Camilo Mayada and Lucas Alario struck in the second half to put River 4-1 up by the 71st minute after Maurice Cova pulled a goal back on the half-hour mark.
Quick-fire goals from Trujillanos pair Franklin Gonzalez and James Cabezas ensured a nervy finale but River held on.