The last four stages of the 2008 Copa Santander Libertadores are the knockout stages: the Round of 16, the Quarterfinals, the Semifinals, and the Finals.

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.

The following criteria will be used for breaking ties on points^[1]:

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.

The Round of 16 was played between April 29 and 30, and May 1, 6, and 8. Team #1 played the second leg at home.

Fluminense advanced 6–0 on points.

LDU Quito 3–3 Estudiantes on points. LDU Quito advanced on better goal difference (+1).

Atlas advanced 4–1 on points.