DrawThe draw of the tournament was held on July 3, 2013 in Buenos Aires, Argentina.
Excluding the defending champion, the other 46 teams were divided into four zones:
- South Zone: Teams from Bolivia, Chile, Paraguay, and Uruguay
- North Zone: Teams from Colombia, Ecuador, Peru, and Venezuela
- Argentina Zone: Teams from Argentina
- Brazil Zone: Teams from Brazil
The draw mechanism was as follows:
- South Zone and North Zone:
- *For the first stage, the 16 teams from the South Zone were drawn into eight ties, and the 16 teams from the North Zone were drawn into the other eight ties. Teams which qualified for berths 1 were drawn against teams which qualified for berths 4, and teams which qualified for berths 2 were drawn against teams which qualified for berths 3, with the former hosting the second leg in both cases. Teams from the same association could not be drawn into the same tie.
- *For the second stage, the 16 winners of the first stage were drawn into eight ties. The eight winners from the South Zone were drawn against the eight winners from the North Zone, with the former hosting the second leg in four ties, and the latter hosting the second leg in the other four ties.
- Argentina Zone: The six teams were drawn into three ties. Teams which qualified for berths 1–3 were drawn against teams which qualified for berths 4–6, with the former hosting the second leg.
- Brazil Zone: The eight teams were split into four ties. No draw was held, where the matchups were based on the berths which the teams qualified for: 1 vs. 8, 2 vs. 7, 3 vs. 6, 4 vs. 5, with the former hosting the second leg.
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".
ScheduleThe schedule of the competition was as follows.
| Stage | First leg | Second leg | | First stage | July 31 | August 7 | | Second stage | August 14, 21 | August 28
September 4 | | Round of 16 | September 18, 25 | September 25
October 2, 23 | | Quarterfinals | October 30 | November 6 | | Semifinals | November 20 | November 27 | | Finals | December 4 | December 11 |
Elimination phaseIn the elimination phase, each tie was played on a home-and-away two-legged basis. If tied on aggregate, the away goals rule was used. If still tied, the penalty shoot-out was used to determine the winner. The 15 winners of the second stage advanced to the round of 16 to join the defending champion.
First stage!colspan=6|South Zone
!colspan=6|North Zone
Final stagesIn the final stages, the 16 teams played a single-elimination tournament, with the following rules:
- Each tie was played on a home-and-away two-legged basis, with the higher-seeded team hosting the second leg.
- In the round of 16, quarterfinals, and semifinals, if tied on aggregate, the away goals rule was used. If still tied, the penalty shoot-out was used to determine the winner.
- In the finals, 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.
- If there were two semifinalists from the same association, they must play each other.
BracketNote: The bracket was changed according to the rules of the tournament so that the two semifinalists from Brazil would play each other.
FinalsThe 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.
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''Lanús won 3–1 on aggregate.''
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