[2] The draw for the second stage was held on 14 June 2017, 20:00 PYT (UTC−4), at the CONMEBOL Convention Center in Luque, Paraguay.
If still tied, extra time would not be played, and the penalty shoot-out would be used to determine the winner (Regulations Article 6.1).
Tied 2–2 on aggregate, Junior won on penalties and advanced to the round of 16 (Match B).
Tied 1–1 on aggregate, LDU Quito won on penalties and advanced to the round of 16 (Match F).
Tied 3–3 on aggregate, Nacional won on away goals and advanced to the round of 16 (Match D).