[2] By winning the competition, Atlético Mineiro won the right to play in the 2013 FIFA Club World Cup and the 2014 Recopa Sudamericana.

The seeding of each team was determined by which associations reached the furthest stage in the previous Copa Libertadores.

[3] Tigre Grêmio São Paulo Iquique Deportes Tolima Olimpia Bolívar LDU Quito León Universidad César Vallejo Defensor Sporting Deportivo Anzoátegui 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).

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 finals were played on a home-and-away two-legged basis, with the higher-seeded team hosting the second leg.