Note: The bracket was adjusted according to the rules of the tournament so that the two Brazilian teams would face each other in the semifinals.
San José 3–3 Newell's Old Boys on points.
Santa Fe 3–3 Atlético Mineiro on points.
LDU Quito 3–3 Unión San Felipe on points.
Note: The second leg was played at a neutral venue since Independiente received a one-match stadium ban after crowd trouble at their home ground during their Round of 16 second leg against Defensor Sporting.
Note: In the final, the away goals rule would not be applied, and extra time would be played if necessary.