In the finals, Argentine team San Lorenzo defeated Paraguayan team Nacional 2–1 on aggregate to win their first title, and earned the right to play in the 2014 FIFA Club World Cup and the 2015 Recopa Sudamericana. The streak of four successive tournaments won by a Brazilian team was broken; in fact, none of the four semifinalists were from Brazil (first time since 1991, and the first finals since 2004 to not feature a Brazilian team) or had reached the final before.
For the first stage, the 12 teams were drawn into six ties containing a team from Pot 1 and a team from Pot 2, with the former hosting the second leg. The seeding of each team was determined by which associations reached the furthest stage in the previous Copa Libertadores.
For the second stage, the 32 teams were drawn into eight groups of four containing one team from each of the four seeding pots. The seeding of each team was determined by their association and qualifying berth (as per the rotational agreement established by CONMEBOL, the teams which qualified through berths 1 from Colombia, Ecuador, Peru and Venezuela were seeded into Pot 1 for odd-numbered years, while the teams which qualified through berths 1 from Bolivia, Chile, Paraguay and Uruguay were seeded into Pot 1 for even-numbered years). Teams from the same association in Pots 1 and 2 could not be drawn into the same group. However, a first stage winner, whose identity was not known at the time of the draw, could be drawn into the same group with another team from the same association.
The schedule of the competition was as follows (all dates listed are Wednesdays, but matches may be played on Tuesdays and Thursdays as well). There was a two-month break between the quarterfinals and semifinals due to the 2014 FIFA World Cup.
In the second stage, each group was played on a home-and-away round-robin basis. Each team earned 3 points for a win, 1 point for a draw, and 0 points for a loss. If tied on points, the following criteria were used to determine the ranking: 1. Goal difference; 2. Goals scored; 3. Away goals scored; 4. Drawing of lots. The winners and runners-up of each group advanced to the round of 16.
Each tie was played on a home-and-away two-legged basis, with the higher-seeded team hosting the second leg. However, CONMEBOL required that the second leg of the finals must be played in South America, i.e., a finalist from Mexico must host the first leg regardless of seeding.
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.