The knockout stages of the 2013 Copa Libertadores de América were played from April 24 to July 24, 2013. A total of 16 teams competed in the knockout stages.
The winners and runners-up of each of the eight groups in the second stage qualified for the knockout stages.
The qualified teams were seeded in the knockout stages according to their results in the second stage, with the group winners seeded 1–8, and the group runners-up seeded 9–16.
Ranking rules: 1. Points; 2. Goal difference; 3. Goals scored; 4. Away goals scored; 5. Drawing of lots.
In the knockout stages, the 16 teams played a single-elimination tournament, with the following rules:
The bracket of the knockout stages was determined by the seeding as follows:
The first legs were played on April 24–25 and April 30–May 2, and the second legs were played on May 8–9 and 14–16, 2013.