| Tuesday 30th July 2013 | |||
| 1st Leg | |||
| Austria Vienna | 1-0 | FH Hafnarfjordur | |
| Basel | 1-0 | Maccabi Tel-Aviv | |
| Dinamo Tbilisi | 0-2 | Steaua Bucharest | |
| Dinamo Zagreb | 1-0 | Sheriff Tiraspol | |
| Lyon | 1-0 | Grasshoppers | |
| Nomme Kalju | 0-4 | Viktoria Plzen | |
| Nordsjaelland | 0-1 | Zenit St Petersburg | |
| PAOK Salonika | 0-2 | Metalist Kharkiv | |
| PSV Eindhoven | 2-0 | Zulte-Waregem | |
| Shakhtyor Karagandy | 3-0 | Skenderbeu | |
| Wednesday 31st July 2013 | |||
| 1st Leg | |||
| Apoel Nicosia | 1-1 | NK Maribor | |
| Celtic | 1-0 | Elfsborg | |
| Ludogorets Razgrad | 2-1 | Partizan Belgrade | |
| Molde | 1-1 | Legia Warsaw | |
| Salzburg | 1-1 | Fenerbahce | |
| Tuesday 6th August 2013 | |||
| 2nd Leg | |||
| Fenerbahce | 3-1 | Salzburg | (4-2) |
| Grasshoppers | 0-1 | Lyon | (0-2) |
| Maccabi Tel-Aviv | 3-3 | Basel | (3-4) |
| NK Maribor | 0-0 | Apoel Nicosia | (1-1) |
| (NK Maribor won on away goals) | |||
| Partizan Belgrade | 0-1 | Ludogorets Razgrad | (1-3) |
| Skenderbeu | 3-2 | Shakhtyor Karagandy | (3-5) |
| Steaua Bucharest | 1-1 | Dinamo Tbilisi | (3-1) |
| Wednesday 7th August 2013 | |||
| 2nd Leg | |||
| Elfsborg | 0-0 | Celtic | (0-1) |
| FH Hafnarfjordur | 0-0 | Austria Vienna | (0-1) |
| Legia Warsaw | 0-0 | Molde | (1-1) |
| (Legia Warsaw won on away goals) | |||
| Metalist Kharkiv | 1-1 | PAOK Salonika | (3-1) |
| Sheriff Tiraspol | 0-3 | Dinamo Zagreb | (0-4) |
| Viktoria Plzen | 6-2 | Nomme Kalju | (10-2) |
| Zenit St Petersburg | 5-0 | Nordsjaelland | (6-0) |
| Zulte-Waregem | 0-3 | PSV Eindhoven | (0-5) |
