The last four stages of the 2009 Copa Santander Libertadores are the knockout stages: the Round of 16, the Quarterfinals, the Semifinals, and the Finals.
Format
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:
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.
^1 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 concerns raised by both Nacional and São Paulo over the Swine flu outbreak in Mexico.
A. ^ Guadalajara and San Luis withdrew from the tournament following concerns raised by both Nacional and São Paulo over the H1N1 flu outbreak in Mexico, South American teams refused to travel to Mexico to play the match; no agreement was reached on alternative venues for the first-leg matches, both scheduled to be played in Mexico. Both Guadalajara and San Luis were later secured a place in the round of 16 for the 2010 Copa Libertadores.