The 1996 Copa Libertadores final stages were played from 30 April to 26 June 1996 and consisted of the round of 16 (or second stage), quarter-finals, semi-finals and the finals. A total of 16 teams competed in the final stages to decide the champions of the 1996 Copa Libertadores.

The winners, runners-up and third placed teams of each of the five groups in the group stage advanced to the round of 16, alongside defending champions Grêmio, who received a direct bye to this round.

In the final stages, the teams were seeded according to the pre-established numbering they received according to the final position they occupied in their respective group. Numbers 1, 5, 9, 13 and 17 correspond to each group winners; numbers 2, 6, 10, 14 and 18 to runners-up; and 3, 7, 11, 15 and 19 to third placed teams.

In the final stages, the 16 teams played a single-elimination tournament with the following rules:

The above criteria were established to ensure that the four semifinalists would be of different nationalities (Regulations Section III, Article 3).

The original bracket for the final stages was determined as follows:

Per regulations, the original bracket had the following modifications:

The first legs were played on 30 April, 1 and 2 May. and the second legs were played on 8 and 9 May 1996.