| Tuesday 16th July 2013 | |||
| 1st Leg | |||
| BATE Borisov | 0-1 | Shakhtyor Karagandy | |
| Birkirkara | 0-0 | NK Maribor | |
| Dinamo Tbilisi | 6-1 | EB Streymur | |
| FK Ekranas Panevezys | 0-1 | FH Hafnarfjordur | |
| Fola Esch | 0-5 | Dinamo Zagreb | |
| Sheriff Tiraspol | 1-1 | Sutjeska Niksic | |
| Steaua Bucharest | 3-0 | FK Vardar Skopje | |
| Viktoria Plzen | 4-3 | Zeljeznicar Sarajevo | |
| Wednesday 17th July 2013 | |||
| 1st Leg | |||
| Cliftonville | 0-3 | Celtic | |
| Elfsborg | 7-1 | Daugava Daugavpils | |
| HJK Helsinki | 0-0 | Nomme Kalju | |
| Neftchi Baku | 0-0 | Skenderbeu | |
| Raba Gyor ETO | 0-2 | Maccabi Tel-Aviv | |
| Shirak Gyumri | 1-1 | Partizan Belgrade | |
| Sligo Rovers | 0-1 | Molde | |
| Slovan Bratislava | 2-1 | Ludogorets Razgrad | |
| The New Saints | 1-3 | Legia Warsaw | |
| Tuesday 23rd July 2013 | |||
| 2nd Leg | |||
| Celtic | 2-0 | Cliftonville | (5-0) |
| Daugava Daugavpils | 0-4 | Elfsborg | (1-11) |
| Dinamo Zagreb | 1-0 | Fola Esch | (6-0) |
| EB Streymur | 1-3 | Dinamo Tbilisi | (2-9) |
| FH Hafnarfjordur | 2-1 | FK Ekranas Panevezys | (3-1) |
| FK Vardar Skopje | 1-2 | Steaua Bucharest | (1-5) |
| Maccabi Tel-Aviv | 2-1 | Raba Gyor ETO | (4-1) |
| Molde | 2-0 | Sligo Rovers | (3-0) |
| Nomme Kalju | 2-1 | HJK Helsinki | (2-1) |
| Shakhtyor Karagandy | 1-0 | BATE Borisov | (2-0) |
| Skenderbeu | 1-0 | Neftchi Baku | aet (1-0) |
| Sutjeska Niksic | 0-5 | Sheriff Tiraspol | (1-6) |
| Zeljeznicar Sarajevo | 1-2 | Viktoria Plzen | (4-6) |
| Wednesday 24th July 2013 | |||
| 2nd Leg | |||
| Legia Warsaw | 1-0 | The New Saints | (4-1) |
| Ludogorets Razgrad | 3-0 | Slovan Bratislava | (4-2) |
| NK Maribor | 2-0 | Birkirkara | (2-0) |
| Partizan Belgrade | 0-0 | Shirak Gyumri | (1-1) |
| (Partizan Belgrade won on away goals) | |||
