| 1st leg | 2nd leg | Agg | |
| Austria Vienna (AUT) vs Hafnarfjordur (ISL) | 1-0 | 0-0 | 1-0 |
| Nordsjalland (DEN) vs Zenit St Petersburg (RUS) | 0-1 | 0-5 | 0-6 |
| PAOK (GRE) vs Metalist Kharkiv (UKR) | 0-2 | 1-1 | 1-3 |
| Dinamo Zagreb (CRO) vs FC Sheriff (MDA) | 1-0 | 3-0 | 4-0 |
| Celtic (SCO) vs Elfsborg (SWE) | 1-0 | 0-0 | 1-0 |
| Nomme Kalju (EST) vs Viktoria Plzen (CZE) | 0-4 | 2-6 | 2-10 |
| Molde FK (NOR) vs Legia Warsaw (POL) (Legia Warsaw through on away goals rule) | 1-1 | 0-0 | 1-1 |
| PSV Eindhoven (NED) vs Zulte Waregem (BEL) | 2-0 | 3-0 | 5-0 |
| Played Tuesday | |||
| Basel (SUI) vs Maccabi Tel-Aviv (ISR) | 1-0 | 3-3 | 4-3 |
| Dinamo Tbilisi (GEO) vs Steaua Bucharest (ROU) | 0-2 | 1-1 | 1-3 |
| APOEL FC (CYP) vs NK Maribor (SVN) (NK Maribor through on away goals rule) | 1-1 | 0-0 | 1-1 |
| Shakhter Karagandy (KAZ) vs Skenderbeu (ALB) | 3-0 | 2-3 | 5-3 |
| Ludogorets (BUL) vs Partizan (SRB) | 2-1 | 1-0 | 3-1 |
| Salzburg (AUT) vs Fenerbahce SK (TUR) | 1-1 | 1-3 | 2-4 |
| Olympique Lyon (FRA) vs Grasshoppers (SUI) | 1-0 | 1-0 | 2-0 |
Note: First-named teams played second legs away.