A 2-0 win at home saw Sao Paulo overcome fellow Brazilian Serie A outfit Criciuma 3-2 on aggregate, booking their spot in the last 16.
Kaka scored the second of two first-half goals as Muricy Ramalho's men completed their comeback victory.
Edson Silva opened the scoring in the 33rd minute at the Estadio Cicero Pompeu de Toledo.
An Osvaldo corner was diverted goal-bound by the defender, finding the bottom corner.
Kaka made it 2-0 four minutes before half-time in fortuitous fashion.
The former Milan star's initial close-range effort was saved by Rodrigo Galatto, only for the rebound to hit him and go in.
Bahia went through after a 1-1 draw at home saw them to a 3-1 aggregate victory over fellow Brazilian outfit Internacional.
Alex gave visitors Internacional hope late in first half, but Henrique's second-half goal saw Bahia to their win.
In the first leg of their second-stage clash, Rosario Central scored a dramatic late equaliser to draw 1-1 at home to fellow Argentine outfit Boca Juniors.
Leandro Marin had Boca on track for an away win after his 37th-minute goal.
Alejandro Donatti saw red for the hosts late on, but substitute Pablo Becker rescued a draw for Rosario Central with a 96th-minute free-kick.
