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| H | Zrinjski Mostar | - | Legia Warszawa | 1:1 (0:0) | ||
| R | Legia Warszawa | - | Zrinjski Mostar | 2:0 (1:0) | ||
| H: 12.07.2016 18:30 | R: 19.07.2016 20:45 | Sieger: Legia Warszawa | ||||
| H | Qarabağ FK | - | F91 Dudelange | 2:0 (2:0) | ||
| R | F91 Dudelange | - | Qarabağ FK | 1:1 (0:0) | ||
| H: 12.07.2016 19:00 | R: 20.07.2016 18:00 | Sieger: Qarabağ FK | ||||
| H | Dinamo Tbilisi | - | FC Alashkert | 2:0 (0:0) | ||
| R | FC Alashkert | - | Dinamo Tbilisi | 1:1 (0:1) | ||
| H: 12.07.2016 19:00 | R: 19.07.2016 17:00 | Sieger: Dinamo Tbilisi | ||||
| H | Hapoel Be'er Sheva | - | FC Sheriff | 3:2 (1:1) | ||
| R | FC Sheriff | - | Hapoel Be'er Sheva | 0:0 (0:0) | ||
| H: 12.07.2016 19:50 | R: 19.07.2016 19:00 | Sieger: Hapoel Be'er Sheva | ||||
| H | The New Saints | - | APOEL Nikosia | 0:0 (0:0) | ||
| R | APOEL Nikosia | - | The New Saints | 3:0 (0:0) | ||
| H: 12.07.2016 20:00 | R: 19.07.2016 19:00 | Sieger: APOEL Nikosia | ||||
| H | BATE Borisov | - | SJK Seinäjoki | 2:0 (1:0) | ||
| R | SJK Seinäjoki | - | BATE Borisov | 2:2 (1:2) | ||
| H: 12.07.2016 20:00 | R: 19.07.2016 19:00 | Sieger: BATE Borisov | ||||
| H | Valletta FC | - | Crvena Zvezda | 1:2 (1:0) | ||
| R | Crvena Zvezda | - | Valletta FC | 2:1 (1:1) | ||
| H: 12.07.2016 20:00 | R: 19.07.2016 20:30 | Sieger: Crvena Zvezda | ||||
| H | Lincoln Red Imps | - | Celtic FC | 1:0 (0:0) | ||
| R | Celtic FC | - | Lincoln Red Imps | 3:0 (3:0) | ||
| H: 12.07.2016 20:00 | R: 20.07.2016 20:45 | Sieger: Celtic FC | ||||
| H | RB Salzburg | - | FK Liepāja | 1:0 (0:0) | ||
| R | FK Liepāja | - | RB Salzburg | 0:2 (0:1) | ||
| H: 12.07.2016 20:30 | R: 19.07.2016 18:00 | Sieger: RB Salzburg | ||||
| H | Vardar Skopje | - | Dinamo Zagreb | 1:2 (0:2) | ||
| R | Dinamo Zagreb | - | Vardar Skopje | 3:2 (0:1) | ||
| H: 12.07.2016 20:45 | R: 20.07.2016 20:45 | Sieger: Dinamo Zagreb | ||||
| H | FK Žalgiris | - | FK Astana | 0:0 (0:0) | ||
| R | FK Astana | - | FK Žalgiris | 2:1 (1:0) | ||
| H: 13.07.2016 19:15 | R: 20.07.2016 16:00 | Sieger: FK Astana | ||||
| H | Rosenborg BK | - | IFK Norrköping | 3:1 (0:0) | ||
| R | IFK Norrköping | - | Rosenborg BK | 3:2 (0:1) | ||
| H: 13.07.2016 19:15 | R: 20.07.2016 19:15 | Sieger: Rosenborg BK | ||||
| H | PFC Ludogorets Razgrad | - | Mladost Podgorica | 2:0 (2:0) | ||
| R | Mladost Podgorica | - | PFC Ludogorets Razgrad | 0:3 (0:1) | ||
| H: 13.07.2016 19:30 | R: 19.07.2016 20:45 | Sieger: PFC Ludogorets Razgrad | ||||
| H | FK Partizani | - | Ferencvárosi TC | 1:1 (0:0) | ||
| R | Ferencvárosi TC | - | FK Partizani | 1:3 (1:1, 1:1, 1:1) i.E. | ||
| H: 13.07.2016 20:00 | R: 20.07.2016 19:30 | Sieger: FK Partizani | ||||
| H | Crusaders FC | - | FC København | 0:3 (0:2) | ||
| R | FC København | - | Crusaders FC | 6:0 (2:0) | ||
| H: 13.07.2016 20:00 | R: 19.07.2016 19:15 | Sieger: FC København | ||||
| H | Olimpija Ljubljana | - | AS Trenčín | 3:4 (2:4) | ||
| R | AS Trenčín | - | Olimpija Ljubljana | 2:3 (2:2) | ||
| H: 13.07.2016 20:30 | R: 20.07.2016 20:15 | Sieger: AS Trenčín | ||||
| H | Dundalk FC | - | FH Hafnarfjörður | 1:1 (0:0) | ||
| R | FH Hafnarfjörður | - | Dundalk FC | 2:2 (1:0) | ||
| H: 13.07.2016 20:45 | R: 20.07.2016 21:15 | Sieger: Dundalk FC | ||||
