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