The draw for the qualifying stages and group stage was held on 21 December 2016, 20:00 PYST, at the CONMEBOL Convention Centre in Luque, Paraguay. Teams were seeded by their CONMEBOL ranking of the Copa Libertadores, taking into account of the following three factors:
Performance in the last 10 years, taking into account Copa Libertadores results in the period 2007–2016
Historical coefficient, taking into account Copa Libertadores results in the period 1960–2006
Local tournament champion, with bonus points awarded to domestic league champions of the last 10 years
For the first stage, the six teams were drawn into three ties, with the seeded teams hosting the second leg.
Seeded
Unseeded
For the second stage, the 16 teams were drawn into eight ties, with the seeded teams hosting the second leg. Teams from the same association could not be drawn into the same tie, excluding the winners of the first stage, which were unseeded and whose identity was not known at the time of the draw, and could be drawn into the same tie with another team from the same association.
Seeded
Unseeded
For the third stage, no draw was made, and the eight teams were allocated into the following four ties, with the second stage winners C5–C8 hosting the second leg. As the identity of the winners of the second stage was not known at the time of the draw, they could be drawn into the same tie with another team from the same association.
In the qualifying stages, each tie was played on a home-and-away two-legged basis. If tied on aggregate, the away goals rule would be used. If still tied, extra time would not be played, and the penalty shoot-out would be used to determine the winner.
Bracket
The qualifying stages were structured as follows:
First stage : The three winners of the first stage advanced to the second stage to join the 13 teams which were given byes to the second stage.
Second stage : The eight winners of the second stage advanced to the third stage.
Third stage : The four winners of the third stage advanced to the group stage to join the 28 direct entrants. The two best teams eliminated in the third stage entered the Copa Sudamericana second stage.
The bracket was decided based on the first stage draw and second stage draw, which were held on 21 December 2016.
Winner G1
Winner G2
Winner G3
Winner G4
First stage
The first legs were played on 23 January, and the second legs were played on 27 January 2017.
Match E1
---- Montevideo Wanderers won 7–5 on aggregate and advanced to the second stage.
The two best teams eliminated in the third stage entered the Copa Sudamericana second stage. Only matches in the third stage were considered for the ranking of teams.
