| Tuesday 24th July 2012 | |||
| Second Qualifying Round 2nd Leg | |||
| Basle | 3-0 | Flora Tallinn | (5-0) |
| Debreceni VSC | 3-0 | Skenderbeu | (3-1) |
| FK Ekranas Panevezys | 2-1 | Shamrock Rovers | (2-1) |
| FK Ventspils | 1-1 | Molde | (1-4) |
| Hapoel Ironi KS | 2-0 | MSK Zilina | (2-1) |
| KR Reykjavik | 1-2 | HJK Helsinki | (1-9) |
| Partizan Belgrade | 3-1 | Valletta | (7-2) |
| Salzburg | 4-3 | F91 Dudelange | (4-4) |
| (F91 Dudelange won on away goals) | |||
| Shakhtar Donetsk | 1-1 | Slovan Liberec | aet (1-2) |
| Sheriff Tiraspol | 1-0 | Ulysses Yerevan | (2-0) |
| Zeljeznicar Sarajevo | 1-2 | NK Maribor | (2-6) |
| Zestafoni | 2-2 | Neftchi Baku | (2-5) |
July 2012
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