A total of 16 teams competed in the final stages to decide the champions of the 2016 Copa Libertadores.
[1] Atlético Nacional won the title by defeating Independiente del Valle in the finals.
Tied 3–3 on aggregate, Independiente del Valle won on penalties and advanced to the semifinals (Match F2).
Tied 2–2 on aggregate, Boca Juniors won on penalties and advanced to the semifinals (Match F2).
The finals were played on a home-and-away two-legged basis, with the higher-seeded team hosting the second leg.