In each stage, the teams will play an opponent in a two-legged tie on a home-away basis.
The team with the most points at the end of each tie will advance.
The remaining two entries will go to Mexican clubs Guadalajara and San Luis.
The following criteria will be used for breaking ties on points: The 16 qualified teams were seeded according to their results in the Second Stage.
Guadalajara and San Luis were given the 13 and 14 seed, respectively, which they had earned in the 2009 Copa Libertadores.
Internacional won the Copa Libertadores on points 6-0.