A 48th-minute goal from Erik saw Goias edge Fluminense 1-0, progressing on the away goals rule after the tie finished locked at 2-2.
Elivelton was sent off just after the hour mark for Fluminense, who were unable to find a way back at the Estadio do Governo do Estado de Goias.
Vitoria joined them in the last 16, beating Sport Recife 2-1 at home to seal a 3-1 aggregate victory in another all-Brazilian tie.
Willie put the hosts ahead in the 22nd minute before Rithiely gave Sport Recife hope of advancing early in the second half.
But Marcinho's goal with 16 minutes remaining sealed the tie for Vitoria, who are bottom of the Brazilian Serie A.
River Plate and Estudiantes are well-placed after the first legs of their respective ties.
German Pezzella's 92nd-minute winner saw Argentine Primera Division leaders River Plate to a 1-0 win at Godoy Cruz.
Estudiantes played out a 0-0 draw at Gimnasia La Plata in their first leg.
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