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| I | Gabala FK | - | Dinamo Moskva | 0:2 (0:1) | ||
| V | Dinamo Moskva | - | Gabala FK | 5:0 (1:0) | ||
| I: 21.09.2016 17:00 | V: 19.10.2016 17:00 | Campeones: Dinamo Moskva | ||||
| I | RB Salzburg | - | Vardar Skopje | 5:0 (3:0) | ||
| V | Vardar Skopje | - | RB Salzburg | 0:3 (0:0) | ||
| I: 27.09.2016 18:00 | V: 19.10.2016 19:00 | Campeones: RB Salzburg | ||||
| I | RSC Anderlecht | - | FC Midtjylland | 0:0 (0:0) | ||
| V | FC Midtjylland | - | RSC Anderlecht | 3:1 (1:0) | ||
| I: 27.09.2016 19:00 | V: 19.10.2016 19:00 | Campeones: FC Midtjylland | ||||
| I | AC Sparta Praha | - | OFK Titograd | 4:0 (3:0) | ||
| V | OFK Titograd | - | AC Sparta Praha | 0:5 (0:3) | ||
| I: 28.09.2016 14:00 | V: 19.10.2016 13:30 | Campeones: AC Sparta Praha | ||||
| I | APOEL Nikosia | - | Roma | 0:3 (0:2) | ||
| V | Roma | - | APOEL Nikosia | 6:1 (2:0) | ||
| I: 28.09.2016 15:00 | V: 19.10.2016 15:30 | Campeones: Roma | ||||
| I | Altınordu FK | - | Levski Sofia | 5:0 (2:0) | ||
| V | Levski Sofia | - | Altınordu FK | 1:1 (1:0) | ||
| I: 28.09.2016 17:00 | V: 19.10.2016 16:00 | Campeones: Altınordu FK | ||||
| I | FC Nitra | - | Málaga | 2:3 (1:0) | ||
| V | Málaga | - | FC Nitra | 5:0 (2:0) | ||
| I: 28.09.2016 18:00 | V: 19.10.2016 18:00 | Campeones: Málaga | ||||
| I | Puskás FC | - | PAOK Saloniki | 1:1 (0:0) | ||
| V | PAOK Saloniki | - | Puskás FC | 0:0 (0:0) | ||
| I: 28.09.2016 18:00 | V: 19.10.2016 17:00 | Campeones: PAOK Saloniki | ||||
| I | NK Domžale | - | FK Čukarički | 1:1 (0:0) | ||
| V | FK Čukarički | - | NK Domžale | 4:1 (1:0) | ||
| I: 28.09.2016 18:00 | V: 19.10.2016 18:00 | Campeones: FK Čukarički | ||||
| I | Breiðablik | - | AFC Ajax | 0:3 (0:2) | ||
| V | AFC Ajax | - | Breiðablik | 4:0 (3:0) | ||
| I: 28.09.2016 18:00 | V: 19.10.2016 19:00 | Campeones: AFC Ajax | ||||
| I | HJK Helsinki | - | Cork City | 0:0 (0:0) | ||
| V | Cork City | - | HJK Helsinki | 1:0 (0:0) | ||
| I: 28.09.2016 18:00 | V: 19.10.2016 20:00 | Campeones: Cork City | ||||
| I | Rosenborg BK | - | AIK Solna | 0:0 (0:0) | ||
| V | AIK Solna | - | Rosenborg BK | 1:3 (1:2) | ||
| I: 28.09.2016 18:00 | V: 19.10.2016 18:00 | Campeones: Rosenborg BK | ||||
| I | FC Viitorul Constanța | - | FC Sheriff | 4:1 (2:1) | ||
| V | FC Sheriff | - | FC Viitorul Constanța | 0:1 (0:1) | ||
| I: 28.09.2016 18:00 | V: 19.10.2016 17:00 | Campeones: FC Viitorul Constanța | ||||
| I | Zrinjski Mostar | - | FC Zürich | 0:3 (0:2) | ||
| V | FC Zürich | - | Zrinjski Mostar | 6:0 (2:0) | ||
| I: 28.09.2016 18:00 | V: 19.10.2016 17:00 | Campeones: FC Zürich | ||||
| I | Dinamo Tbilisi | - | FK Kairat | 0:3 (0:0) | ||
| V | FK Kairat | - | Dinamo Tbilisi | 5:1 (0:1) | ||
| I: 29.09.2016 18:00 | V: 19.10.2016 15:00 | Campeones: FK Kairat | ||||
| I | Maccabi Haifa | - | Shakhter Soligorsk | 5:0 (1:0) | ||
| V | Shakhter Soligorsk | - | Maccabi Haifa | 2:3 (0:3) | ||
| I: 05.10.2016 17:00 | V: 19.10.2016 18:00 | Campeones: Maccabi Haifa | ||||
