| 3. Round | 24/08/2012 | Hertha BSC | - | Jahn Regensburg | 2:1 | ||||
| 5. Round | 15/09/2012 | Eintracht Braunschweig | - | Jahn Regensburg | 1:0 | ||||
| 6. Round | 22/09/2012 | Jahn Regensburg | - | Energie Cottbus | 0:1 | ||||
| 7. Round | 25/09/2012 | SV Sandhausen | - | Jahn Regensburg | 1:2 |  |
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| 8. Round | 28/09/2012 | Jahn Regensburg | - | FC St. Pauli | 3:0 | |
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| 9. Round | 07/10/2012 | Erzgebirge Aue | - | Jahn Regensburg | 3:1 | ||||
| 10. Round | 20/10/2012 | Jahn Regensburg | - | 1. FC Köln | 2:3 | |
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| 11. Round | 28/10/2012 | FSV Frankfurt | - | Jahn Regensburg | 3:1 | ||||
| 12. Round | 02/11/2012 | Jahn Regensburg | - | SC Paderborn 07 | 0:2 | ||||
| 13. Round | 11/11/2012 | FC Ingolstadt 04 | - | Jahn Regensburg | 4:2 | ||||
| 17. Round | 30/11/2012 | Jahn Regensburg | - | Dynamo Dresden | 0:0 | ||||
| 26. Round | 17/03/2013 | Jahn Regensburg | - | Erzgebirge Aue | 1:1 |  |
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| 31. Round | 26/04/2013 | 1. FC Union Berlin | - | Jahn Regensburg | 1:0 | ||||
| 32. Round | 03/05/2013 | VfR Aalen | - | Jahn Regensburg | 2:1 | |
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| 33. Round | 12/05/2013 | Jahn Regensburg | - | 1. FC Kaiserslautern | 1:3 | ||||
| 34. Round | 19/05/2013 | Dynamo Dresden | - | Jahn Regensburg | 3:1 |
Germany