The 2016 Copa Sudamericana final stages were scheduled to be played from 20 September to 7 December 2016.
A total of 16 teams competed in the final stages to decide the champions of the 2016 Copa Sudamericana.
[6] Tied 3–3 on aggregate, Independiente Medellín won on away goals and advanced to the quarterfinals (Match S1).
[8] Tied 1–1 on aggregate, Atlético Nacional won on away goals and advanced to the finals.
The final would be played on a home-and-away two-legged basis, with the higher-seeded team hosting the second leg.
If tied on aggregate, the away goals rule would not be used, and 30 minutes of extra time would be played.