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| U | PAOK Saloniki | - | AFC Ajax | 0:2 (0:1) | ||
| R | AFC Ajax | - | PAOK Saloniki | 2:1 (0:0) | ||
| U: 02.11.2016 14:00 | R: 22.11.2016 19:00 | Winnaars: AFC Ajax | ||||
| U | FC Viitorul Constanța | - | FC Zürich | 5:0 (2:0) | ||
| R | FC Zürich | - | FC Viitorul Constanța | 2:0 (2:0) | ||
| U: 02.11.2016 17:00 | R: 23.11.2016 17:00 | Winnaars: FC Viitorul Constanța | ||||
| U | Málaga CF | - | FC Midtjylland | 2:0 (0:0) | ||
| R | FC Midtjylland | - | Málaga CF | 4:0 (2:0) | ||
| U: 02.11.2016 18:00 | R: 23.11.2016 19:00 | Winnaars: FC Midtjylland | ||||
| U | Rosenborg BK | - | FK Čukarički | 0:1 (0:0) | ||
| R | FK Čukarički | - | Rosenborg BK | 0:2 (0:0) | ||
| U: 02.11.2016 18:00 | R: 23.11.2016 18:00 | Winnaars: Rosenborg BK | ||||
| U | RB Salzburg | - | FK Kairat | 8:1 (2:0) | ||
| R | FK Kairat | - | RB Salzburg | 0:1 (0:1) | ||
| U: 02.11.2016 18:00 | R: 23.11.2016 14:00 | Winnaars: RB Salzburg | ||||
| U | Cork City | - | AS Roma | 1:3 (1:1) | ||
| R | AS Roma | - | Cork City | 1:0 (0:0) | ||
| U: 02.11.2016 20:00 | R: 23.11.2016 15:00 | Winnaars: AS Roma | ||||
| U | Altınordu FK | - | Sparta Praag | 6:2 (3:1) | ||
| R | Sparta Praag | - | Altınordu FK | 3:2 (0:1) | ||
| U: 09.11.2016 14:00 | R: 30.11.2016 15:00 | Winnaars: Altınordu FK | ||||
| U | Maccabi Haifa | - | Dinamo Moskva | 0:0 (0:0) | ||
| R | Dinamo Moskva | - | Maccabi Haifa | 1:1 (0:0) | ||
| U: 16.11.2016 16:00 | R: 23.11.2016 11:30 | Winnaars: Maccabi Haifa | ||||
