Time Zone – GMT-5 (America/New_York)
| Pl | W | D | L | Diff | Pts | |||
| 1 | Lyon | 5 | 4 | 0 | 1 | 11:2 | 9 | 12 |
| 2 | Midtjylland | 5 | 4 | 0 | 1 | 12:5 | 7 | 12 |
| 3 | Aston Villa | 5 | 4 | 0 | 1 | 8:3 | 5 | 12 |
| 4 | Freiburg | 5 | 3 | 2 | 0 | 8:3 | 5 | 11 |
| 5 | Betis | 5 | 3 | 2 | 0 | 8:3 | 5 | 11 |
| 6 | Ferencvaros | 5 | 3 | 2 | 0 | 9:5 | 4 | 11 |
| 7 | Braga | 5 | 3 | 1 | 1 | 9:5 | 4 | 10 |
| 8 | FC Porto | 5 | 3 | 1 | 1 | 7:4 | 3 | 10 |
| 9 | Genk | 5 | 3 | 1 | 1 | 7:5 | 2 | 10 |
| 10 | Celta Vigo | 5 | 3 | 0 | 2 | 11:7 | 4 | 9 |
| 11 | Lille | 5 | 3 | 0 | 2 | 10:6 | 4 | 9 |
| 12 | Stuttgart | 5 | 3 | 0 | 2 | 8:4 | 4 | 9 |
| 13 | Plzen | 5 | 2 | 3 | 0 | 6:2 | 4 | 9 |
| 14 | Panathinaikos | 5 | 3 | 0 | 2 | 9:7 | 2 | 9 |
| 15 | AS Roma | 5 | 3 | 0 | 2 | 7:5 | 2 | 9 |
| 16 | Nottingham | 5 | 2 | 2 | 1 | 9:5 | 4 | 8 |
| 17 | PAOK | 5 | 2 | 2 | 1 | 10:7 | 3 | 8 |
| 18 | Bologna | 5 | 2 | 2 | 1 | 7:4 | 3 | 8 |
| 19 | Brann | 5 | 2 | 2 | 1 | 6:3 | 3 | 8 |
| 20 | Fenerbahce | 5 | 2 | 2 | 1 | 5:5 | 0 | 8 |
| 21 | Celtic | 5 | 2 | 1 | 2 | 7:8 | -1 | 7 |
| 22 | Crvena zvezda | 5 | 2 | 1 | 2 | 4:5 | -1 | 7 |
| 23 | Din. Zagreb | 5 | 2 | 1 | 2 | 7:10 | -3 | 7 |
| 24 | Basel | 5 | 2 | 0 | 3 | 7:7 | 0 | 6 |
| 25 | Ludogorets | 5 | 2 | 0 | 3 | 8:11 | -3 | 6 |
| 26 | Young Boys | 5 | 2 | 0 | 3 | 7:12 | -5 | 6 |
| 27 | G.A. Eagles | 5 | 2 | 0 | 3 | 4:9 | -5 | 6 |
| 28 | Sturm Graz | 5 | 1 | 1 | 3 | 4:7 | -3 | 4 |
| 29 | Salzburg | 5 | 1 | 0 | 4 | 5:10 | -5 | 3 |
| 30 | Feyenoord | 5 | 1 | 0 | 4 | 4:9 | -5 | 3 |
| 31 | FCSB | 5 | 1 | 0 | 4 | 3:8 | -5 | 3 |
| 32 | Utrecht | 5 | 0 | 1 | 4 | 2:7 | -5 | 1 |
| 33 | Rangers | 5 | 0 | 1 | 4 | 2:9 | -7 | 1 |
| 34 | Malmo FF | 5 | 0 | 1 | 4 | 2:10 | -8 | 1 |
| 35 | Maccabi Tel Aviv | 5 | 0 | 1 | 4 | 1:14 | -13 | 1 |
| 36 | Nice | 5 | 0 | 0 | 5 | 4:12 | -8 | 0 |
| 1 | Hamrun | Bye | |
| 4 | Bye | Maccabi Tel Aviv | |
| 8 | Bye | Dyn. Kyiv | |
| 9 | Shkendija | Bye | |
| 16 | Bye | Ludogorets | |
| 17 | Slovan Bratislava | Bye | |
| 24 | Bye | Young Boys | |
| 25 | Malmo FF | Bye | |
| 32 | Bye | Sigma Olomouc | |
| 33 | Panathinaikos | Bye | |
| 35 | Besiktas | Bye | |
| 36 | Shakhtar Donetsk | Ilves | 0 : 0, 6 : 0 |
| 40 | Bye | Samsunspor | |
| 41 | Aberdeen | Bye | |
| 45 | FCSB | Bye | |
| 48 | Bye | Drita | |
| 49 | Lech Poznan | Bye | |
| 56 | Bye | Genk | |
| 57 | Fredrikstad | Bye | |
| 59 | Midtjylland | Bye | |
| 60 | Bye | Hibernian | |
| 61 | RFS | Bye | |
| 64 | Bye | KuPS | |
| 65 | Lincoln Red Imps | Bye | |
| 68 | Bye | Noah | |
| 69 | Lugano | Bye | |
| 70 | Paks | CFR Cluj | 0 : 3, 0 : 0 |
| 71 | Levski Sofia | H. Beer Sheva | 2 : 1, 0 : 0 |
| 72 | Bye | Braga | |
| 73 | Zrinjski | Bye | |
| 76 | Bye | Breidablik | |
| 77 | Servette | Bye | |
| 79 | Sheriff Tiraspol | Prishtina | 1 : 2, 4 : 0 |
| 80 | Bye | Utrecht | |
| 81 | Anderlecht | Bye | |
| 82 | Trnava | Hacken | 2 : 2, 0 : 1 |
| 84 | Bye | Brann | |
| 85 | Sabah Baku | Celje | 3 : 3, 2 : 3 |
| 86 | AEK Larnaca | Partizan | 2 : 2, 1 : 0 |
| 87 | Ostrava | Bye | |
| 88 | Legia | Aktobe | 1 : 0, 1 : 0 |
| 89 | Rijeka | Bye | |
| 92 | Bye | Shelbourne | |
| 93 | PAOK | Bye | |
| 96 | Bye | Wolfsberger AC |
| 1 | Hamrun | Bye | |
| 2 | Bye | Maccabi Tel Aviv | |
| 4 | Bye | Dyn. Kyiv | |
| 5 | Shkendija | Bye | |
| 8 | Bye | Ludogorets | |
| 9 | Slovan Bratislava | Bye | |
| 12 | Bye | Young Boys | |
| 13 | Malmo FF | Bye | |
| 16 | Bye | Sigma Olomouc | |
| 17 | Panathinaikos | Bye | |
| 18 | Besiktas | Shakhtar Donetsk | 0 : 2, 2 : 4 |
| 20 | Bye | Samsunspor | |
| 21 | Aberdeen | Bye | |
| 23 | FCSB | Bye | |
| 24 | Bye | Drita | |
| 25 | Lech Poznan | Bye | |
| 28 | Bye | Genk | |
| 29 | Fredrikstad | Bye | |
| 30 | Midtjylland | Hibernian | 2 : 1, 1 : 1 |
| 31 | RFS | Bye | |
| 32 | Bye | KuPS | |
| 33 | Lincoln Red Imps | Bye | |
| 34 | Bye | Noah | |
| 35 | Lugano | CFR Cluj | 0 : 1, 0 : 0 |
| 36 | Levski Sofia | Braga | 0 : 1, 0 : 0 |
| 37 | Zrinjski | Bye | |
| 38 | Bye | Breidablik | |
| 39 | Servette | Bye | |
| 40 | Sheriff Tiraspol | Utrecht | 1 : 4, 1 : 3 |
| 41 | Anderlecht | Hacken | 1 : 3, 1 : 0 |
| 42 | Bye | Brann | |
| 43 | Celje | AEK Larnaca | 1 : 2, 1 : 1 |
| 44 | Ostrava | Legia | 1 : 2, 2 : 2 |
| 45 | Rijeka | Bye | |
| 46 | Bye | Shelbourne | |
| 47 | PAOK | Bye | |
| 48 | Bye | Wolfsberger AC |
| 1 | Hamrun | Maccabi Tel Aviv | 1 : 3, 1 : 2 |
| 2 | Bye | Dyn. Kyiv | |
| 3 | Shkendija | Bye | |
| 4 | Bye | Ludogorets | |
| 5 | Slovan Bratislava | Bye | |
| 6 | Bye | Young Boys | |
| 7 | Malmo FF | Bye | |
| 8 | Bye | Sigma Olomouc | |
| 9 | Panathinaikos | Shakhtar Donetsk | 1 : 0, 0 : 0 |
| 10 | Bye | Samsunspor | |
| 11 | Aberdeen | Bye | |
| 12 | FCSB | Drita | 3 : 1, 3 : 2 |
| 13 | Lech Poznan | Bye | |
| 14 | Bye | Genk | |
| 15 | Fredrikstad | Midtjylland | 0 : 2, 1 : 3 |
| 16 | RFS | KuPS | 0 : 1, 1 : 2 |
| 17 | Lincoln Red Imps | Noah | 1 : 0, 1 : 1 |
| 18 | CFR Cluj | Braga | 0 : 2, 1 : 2 |
| 19 | Zrinjski | Breidablik | 2 : 1, 1 : 1 |
| 20 | Servette | Utrecht | 1 : 2, 1 : 3 |
| 21 | Hacken | Brann | 1 : 0, 0 : 2 |
| 22 | AEK Larnaca | Legia | 1 : 2, 4 : 1 |
| 23 | Rijeka | Shelbourne | 3 : 1, 1 : 2 |
| 24 | PAOK | Wolfsberger AC | 1 : 0, 0 : 0 |
| 1 | Maccabi Tel Aviv | Dyn. Kyiv | 0 : 1, 3 : 1 |
| 2 | Shkendija | Ludogorets | 1 : 4, 2 : 1 |
| 3 | Slovan Bratislava | Young Boys | 2 : 3, 0 : 1 |
| 4 | Malmo FF | Sigma Olomouc | 2 : 0, 3 : 0 |
| 5 | Panathinaikos | Samsunspor | 0 : 0, 2 : 1 |
| 6 | Aberdeen | FCSB | 0 : 3, 2 : 2 |
| 7 | Lech Poznan | Genk | 2 : 1, 1 : 5 |
| 8 | Midtjylland | KuPS | 2 : 0, 4 : 0 |
| 9 | Lincoln Red Imps | Braga | 1 : 5, 0 : 4 |
| 10 | Zrinjski | Utrecht | 0 : 0, 0 : 2 |
| 11 | Brann | AEK Larnaca | 4 : 0, 2 : 1 |
| 12 | Rijeka | PAOK | 0 : 5, 1 : 0 |
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