The remaining stages of the tournament constitute a single-elimination tournament. In each stage, the teams will play an opponent in a two-legged tie on a home-away basis. Each team will earn three points for a win, one point for a draw, and zero points for a loss. The team with the most points at the end of each tie will advance.
Tie-breaking
The following criteria will be used for breaking ties on points:
Goal difference
Goals scored
Away goals
Penalty shootout
Seeding
The 16 qualified teams in the knockout round will be seeded according to their results in the group stage. The top teams from each group are seeded 1-8, with the team with the most points as seed 1 and the team with the least as seed 8. The second-best teams from each group are seeded 9-16, with the team with the most points as seed 9 and the team with the least as seed 16. Teams with a higher seed will play the second leg of each tie at home.
Bracket
Round of 16
The Round of 16 began on May 5. Team #1, as the higher seeded team, played the second leg at home.
Guadalajara and San Luis withdrew from the tournament after an agreement on an alternative venue for the first legs, both scheduled to be played in Mexico, was unable to be agreed upon following concernsraised by both Nacional and São Paulo over the Swine flu outbreak in Mexico.
Team #1, as the higher seed, will play the second leg at home.
First leg
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Second leg
Nacional 2–2 Palmeiras on points. Nacional and Palmeiras tied on goal difference and goals scored. Nacional advances on away goals. ---- Grêmio 2−2 Caracas on points. Grêmio and Caracas tied on goal difference and goals scored. Grêmio advances on away goals. ---- Estudiantes advances 6–0 on points. ---- Cruzeiro advances 6–0 on points.
Semifinals
First leg
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Second leg
Estudiantes advances 6–0 on points. ---- Cruzeiro advances 4–1 on points.
