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| 1st(1st leg) | Viktoria Plzeň | - | Željezničar Sarajevo | 4:3 (0:0) | ||
| 2nd (2nd leg) | Željezničar Sarajevo | - | Viktoria Plzeň | 1:2 (1:2) | ||
| 1st(1st leg): 16/07/2013 16:30 | 2nd (2nd leg): 23/07/2013 20:00 | Winner: Viktoria Plzeň | ||||
| 1st(1st leg) | BATE Borisov | - | Shakter Karaganda | 0:1 (0:0) | ||
| 2nd (2nd leg) | Shakter Karaganda | - | BATE Borisov | 1:0 (0:0) | ||
| 1st(1st leg): 16/07/2013 17:00 | 2nd (2nd leg): 23/07/2013 14:30 | Winner: Shakter Karaganda | ||||
| 1st(1st leg) | Dinamo Tbilisi | - | EB/Streymur | 6:1 (2:1) | ||
| 2nd (2nd leg) | EB/Streymur | - | Dinamo Tbilisi | 1:3 (1:2) | ||
| 1st(1st leg): 16/07/2013 17:00 | 2nd (2nd leg): 23/07/2013 19:00 | Winner: Dinamo Tbilisi | ||||
| 1st(1st leg) | FC Sheriff | - | FK Sutjeska | 1:1 (1:0) | ||
| 2nd (2nd leg) | FK Sutjeska | - | FC Sheriff | 0:5 (0:1) | ||
| 1st(1st leg): 16/07/2013 18:00 | 2nd (2nd leg): 23/07/2013 16:30 | Winner: FC Sheriff | ||||
| 1st(1st leg) | FK Ekranas | - | FH Hafnarfjörður | 0:1 (0:1) | ||
| 2nd (2nd leg) | FH Hafnarfjörður | - | FK Ekranas | 2:1 (1:1) | ||
| 1st(1st leg): 16/07/2013 18:00 | 2nd (2nd leg): 23/07/2013 20:15 | Winner: FH Hafnarfjörður | ||||
| 1st(1st leg) | Birkirkara FC | - | NK Maribor | 0:0 (0:0) | ||
| 2nd (2nd leg) | NK Maribor | - | Birkirkara FC | 2:0 (1:0) | ||
| 1st(1st leg): 16/07/2013 18:30 | 2nd (2nd leg): 24/07/2013 19:00 | Winner: NK Maribor | ||||
| 1st(1st leg) | CS FOLA Esch | - | Dinamo Zagreb | 0:5 (0:0) | ||
| 2nd (2nd leg) | Dinamo Zagreb | - | CS FOLA Esch | 1:0 (0:0) | ||
| 1st(1st leg): 16/07/2013 18:30 | 2nd (2nd leg): 23/07/2013 19:45 | Winner: Dinamo Zagreb | ||||
| 1st(1st leg) | FC Steaua Bucureşti | - | Vardar Skopje | 3:0 (3:0) | ||
| 2nd (2nd leg) | Vardar Skopje | - | FC Steaua Bucureşti | 1:2 (1:1) | ||
| 1st(1st leg): 16/07/2013 18:45 | 2nd (2nd leg): 23/07/2013 19:45 | Winner: FC Steaua Bucureşti | ||||
| 1st(1st leg) | Shirak FC | - | Partizan | 1:1 (0:0) | ||
| 2nd (2nd leg) | Partizan | - | Shirak FC | 0:0 (0:0) | ||
| 1st(1st leg): 17/07/2013 14:00 | 2nd (2nd leg): 24/07/2013 19:45 | Winner: Partizan | ||||
| 1st(1st leg) | HJK Helsinki | - | JK Nõmme Kalju | 0:0 (0:0) | ||
| 2nd (2nd leg) | JK Nõmme Kalju | - | HJK Helsinki | 2:1 (2:0) | ||
| 1st(1st leg): 17/07/2013 16:30 | 2nd (2nd leg): 23/07/2013 16:30 | Winner: JK Nõmme Kalju | ||||
| 1st(1st leg) | Neftçi PFK | - | KF Skënderbeu | 0:0 (0:0) | ||
| 2nd (2nd leg) | KF Skënderbeu | - | Neftçi PFK | 1:0 (0:0, 0:0) aet | ||
| 1st(1st leg): 17/07/2013 17:00 | 2nd (2nd leg): 23/07/2013 19:00 | Winner: KF Skënderbeu | ||||
| 1st(1st leg) | Sligo Rovers | - | Molde FK | 0:1 (0:1) | ||
| 2nd (2nd leg) | Molde FK | - | Sligo Rovers | 2:0 (1:0) | ||
| 1st(1st leg): 17/07/2013 18:00 | 2nd (2nd leg): 23/07/2013 18:00 | Winner: Molde FK | ||||
| 1st(1st leg) | IF Elfsborg | - | FC Daugava | 7:1 (1:0) | ||
| 2nd (2nd leg) | FC Daugava | - | IF Elfsborg | 0:4 (0:1) | ||
| 1st(1st leg): 17/07/2013 18:00 | 2nd (2nd leg): 23/07/2013 16:00 | Winner: IF Elfsborg | ||||
| 1st(1st leg) | The New Saints | - | Legia Warszawa | 1:3 (1:0) | ||
| 2nd (2nd leg) | Legia Warszawa | - | The New Saints | 1:0 (0:0) | ||
| 1st(1st leg): 17/07/2013 19:15 | 2nd (2nd leg): 24/07/2013 19:45 | Winner: Legia Warszawa | ||||
| 1st(1st leg) | Slovan Bratislava | - | PFC Ludogorets Razgrad | 2:1 (0:0) | ||
| 2nd (2nd leg) | PFC Ludogorets Razgrad | - | Slovan Bratislava | 3:0 (2:0) | ||
| 1st(1st leg): 17/07/2013 19:15 | 2nd (2nd leg): 24/07/2013 18:30 | Winner: PFC Ludogorets Razgrad | ||||
| 1st(1st leg) | Győri ETO FC | - | Maccabi Tel Aviv | 0:2 (0:0) | ||
| 2nd (2nd leg) | Maccabi Tel Aviv | - | Győri ETO FC | 2:1 (1:0) | ||
| 1st(1st leg): 17/07/2013 19:30 | 2nd (2nd leg): 23/07/2013 19:30 | Winner: Maccabi Tel Aviv | ||||
| 1st(1st leg) | Cliftonville FC | - | Celtic FC | 0:3 (0:2) | ||
| 2nd (2nd leg) | Celtic FC | - | Cliftonville FC | 2:0 (1:0) | ||
| 1st(1st leg): 17/07/2013 19:45 | 2nd (2nd leg): 23/07/2013 19:45 | Winner: Celtic FC | ||||
