| 4. Round | 02/09/2012 | Jahn Regensburg | - | VfL Bochum | 0:1 | ||||
| 6. Round | 22/09/2012 | Jahn Regensburg | - | Energie Cottbus | 0:1 | ||||
| 7. Round | 25/09/2012 | SV Sandhausen | - | Jahn Regensburg | 1:2 | ||||
| 8. Round | 28/09/2012 | Jahn Regensburg | - | FC St. Pauli | 3:0 | ||||
| 9. Round | 07/10/2012 | Erzgebirge Aue | - | Jahn Regensburg | 3:1 | ||||
| 10. Round | 20/10/2012 | Jahn Regensburg | - | 1. FC Köln | 2:3 | ||||
| 11. Round | 28/10/2012 | FSV Frankfurt | - | Jahn Regensburg | 3:1 | ||||
| 12. Round | 02/11/2012 | Jahn Regensburg | - | SC Paderborn 07 | 0:2 | ||||
| 20. Round | 03/02/2013 | Jahn Regensburg | - | Hertha BSC | 1:5 | ||||
| 21. Round | 10/02/2013 | VfL Bochum | - | Jahn Regensburg | 0:2 |  |
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| 22. Round | 15/02/2013 | Jahn Regensburg | - | Eintracht Braunschweig | 0:1 | ||||
| 24. Round | 01/03/2013 | Jahn Regensburg | - | SV Sandhausen | 1:3 | ||||
| 25. Round | 08/03/2013 | FC St. Pauli | - | Jahn Regensburg | 3:2 | ||||
| 26. Round | 17/03/2013 | Jahn Regensburg | - | Erzgebirge Aue | 1:1 | ||||
| 27. Round | 31/03/2013 | 1. FC Köln | - | Jahn Regensburg | 2:1 | |
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| 28. Round | 06/04/2013 | Jahn Regensburg | - | FSV Frankfurt | 1:4 |
Austria