The 2016 Copa Libertadores final stages were played from 26 April to 27 July 2016. 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.
The winners and runners-up of each of the eight groups in the second stage qualified for the final stages.
| Group | width=200 | Winners | width=200 | Runners-up |
|---|---|---|---|---|
| 1 |  River Plate |  São Paulo | ||
| 2 | Rosario Central | Nacional | ||
| 3 | Boca Juniors | Racing | ||
| 4 |  Atlético Nacional | Huracán | ||
| 5 | Atlético Mineiro |  Independiente del Valle | ||
| 6 |  Toluca | Grêmio | ||
| 7 | UNAM |  Deportivo Táchira | ||
| 8 | Corinthians | Cerro Porteño |
The qualified teams were seeded in the final stages according to their results in the second stage, with the group winners seeded 1–8, and the group runners-up seeded 9–16.
In the final stages, the 16 teams played a single-elimination tournament, with the following rules:[1]
The first legs were played on 26–28 April, and the second legs were played on 3–5 May 2016.[2] |}
----Atlético Nacional won 4–2 on aggregate and advanced to the quarterfinals (Match S1).
----UNAM won 2–1 on aggregate and advanced to the quarterfinals (Match S2).
----Tied 2–2 on aggregate, Nacional won on away goals and advanced to the quarterfinals (Match S3).
----Atlético Mineiro won 2–1 on aggregate and advanced to the quarterfinals (Match S4).
----São Paulo won 5–3 on aggregate and advanced to the quarterfinals (Match S4).
----Boca Juniors won 5–2 on aggregate and advanced to the quarterfinals (Match S3).
----Independiente del Valle won 2–1 on aggregate and advanced to the quarterfinals (Match S2).
----Rosario Central won 4–0 on aggregate and advanced to the quarterfinals (Match S1).
The first legs were played on 11–12 and 17 May, and the second legs were played on 18–19 and 24 May 2016.[3] |}
----Atlético Nacional won 3–2 on aggregate and advanced to the semifinals (Match F1).
----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).
----Tied 2–2 on aggregate, São Paulo won on away goals and advanced to the semifinals (Match F1).
The first legs were played on 6–7 July, and the second legs were played on 13–14 July 2016.[4] |}
----Atlético Nacional won 4–1 on aggregate and advanced to the finals.
----Independiente del Valle won 5–3 on aggregate and advanced to the finals.
See main article: article and 2016 Copa Libertadores Finals.
The first leg was played on 20 July, and the second leg was played on 27 July 2016.[5]