| 1. Round | 05/08/2012 | MSV Duisburg | - | VfR Aalen | 1:4 | ||||
| 2. Round | 12/08/2012 | Jahn Regensburg | - | MSV Duisburg | 2:0 | ||||
| 3. Round | 25/08/2012 | MSV Duisburg | - | Dynamo Dresden | 1:3 | ||||
| 9. Round | 06/10/2012 | Energie Cottbus | - | MSV Duisburg | 0:1 | ||||
| 10. Round | 19/10/2012 | MSV Duisburg | - | FC Ingolstadt 04 | 0:2 | ||||
| 11. Round | 27/10/2012 | SV Sandhausen | - | MSV Duisburg | 0:2 | ||||
| 12. Round | 03/11/2012 | MSV Duisburg | - | FSV Frankfurt | 1:2 | ||||
| 13. Round | 09/11/2012 | 1. FC Köln | - | MSV Duisburg | 0:0 | ||||
| 14. Round | 18/11/2012 | MSV Duisburg | - | Erzgebirge Aue | 2:1 | ||||
| 15. Round | 25/11/2012 | FC St. Pauli | - | MSV Duisburg | 4:1 |  |
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| 17. Round | 02/12/2012 | SC Paderborn 07 | - | MSV Duisburg | 0:2 | ||||
| 18. Round | 07/12/2012 | VfR Aalen | - | MSV Duisburg | 0:1 | ||||
| 19. Round | 16/12/2012 | MSV Duisburg | - | Jahn Regensburg | 4:2 |
Croatia