The final stages of the 2013 Copa Sudamericana were played from September 18 to December 11, 2013. A total of 16 teams competed in the final stages.[1]
The draw of the tournament was held on July 3, 2013, 12:00 UTC−3, at the Sheraton Hotel in Buenos Aires, Argentina.[2]
To determine the bracket starting from the round of 16, the defending champion and the 15 winners of the second stage were assigned a "seed" by draw. The defending champion and the winners from Argentina Zone and Brazil Zone were assigned even-numbered "seeds", and the winners from ties between South Zone and North Zone were assigned odd-numbered "seeds".
The following were the seeding of the 16 teams which qualified for the final stages, which included the defending champion (São Paulo) and the 15 winners of the second stage (three from Argentina Zone, four from Brazil Zone, eight from ties between South Zone and North Zone):
| Seed | width=190 | Team |
|---|---|---|
| 1 | Universidad Católica | |
| 2 |  River Plate | |
| 3 |  Deportivo Pasto | |
| 4 |  Sport Recife | |
| 5 | Itagüí | |
| 6 | Vélez Sarsfield | |
| 7 | Universidad de Chile | |
| 8 | Bahia | |
| 9 | Atlético Nacional | |
| 10 | Lanús | |
| 11 | La Equidad | |
| 12 | Coritiba | |
| 13 | Libertad | |
| 14 | Ponte Preta | |
| 15 |  LDU Loja | |
| 16 | São Paulo |
In the final stages, the 16 teams played a single-elimination tournament, with the following rules:[1]
The bracket of the knockout stages was determined by the seeding as follows:[1]
Note: The bracket was changed according to the rules of the tournament so that the two semifinalists from Brazil would play each other.
The first legs were played on September 18–19 and 24–26, and the second legs were played on September 25–26, October 2 and 22–24, 2013.[3] [4]
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----São Paulo won 5–4 on aggregate.
----River Plate won 3–2 on aggregate.
----Ponte Preta won 2–1 on aggregate.
----Libertad won 4–1 on aggregate.
----Itagüí won 3–1 on aggregate.
----Vélez Sarsfield won 4–2 on aggregate.
----Lanús won 4–1 on aggregate.
----Tied 1–1 on aggregate, Atlético Nacional won on penalties.
The first legs were played on October 29–31, and the second legs were played on November 6–7, 2013.[5]
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----São Paulo won 3–2 on aggregate.
----Lanús won 3–1 on aggregate.
----Ponte Preta won 2–0 on aggregate.
----Libertad won 2–1 on aggregate.
The first legs were played on November 20–21, and the second legs were played on November 27–28, 2013.[6]
A minute of silence was held in honor to the passing of two-time World Cup-winning Brazilian player Nílton Santos at both second leg games of the semifinals.[7]
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----Ponte Preta won 4–2 on aggregate.
----Lanús won 4–2 on aggregate.
See main article: 2013 Copa Sudamericana Finals.
The finals were 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 was not used, and 30 minutes of extra time was played. If still tied after extra time, the penalty shoot-out was used to determine the winner.[1]
The first leg was played on December 4, and the second leg was played on December 11, 2013.[8]
----Lanús won 3–1 on aggregate.