| 1. Round | 03/08/2012 | Erzgebirge Aue | - | FC St. Pauli | 0:0 | ||||
| 2. Round | 11/08/2012 | FC St. Pauli | - | FC Ingolstadt 04 | 1:1 | ||||
| 14. Round | 19/11/2012 | Hertha BSC | - | FC St. Pauli | 1:0 |  |
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| 17. Round | 01/12/2012 | FC St. Pauli | - | 1. FC Kaiserslautern | 1:0 | ||||
| 18. Round | 09/12/2012 | FC St. Pauli | - | Erzgebirge Aue | 0:3 | ||||
| 20. Round | 03/02/2013 | FC St. Pauli | - | Energie Cottbus | 0:0 | ||||
| 21. Round | 10/02/2013 | SV Sandhausen | - | FC St. Pauli | 4:1 | ||||
| 22. Round | 18/02/2013 | FC St. Pauli | - | 1. FC Köln | 0:1 | ||||
| 23. Round | 22/02/2013 | FC St. Pauli | - | FSV Frankfurt | 3:0 | ||||
| 24. Round | 03/03/2013 | VfR Aalen | - | FC St. Pauli | 0:1 | ||||
| 26. Round | 15/03/2013 | 1. FC Union Berlin | - | FC St. Pauli | 4:2 | ||||
| 27. Round | 01/04/2013 | FC St. Pauli | - | SC Paderborn 07 | 2:2 | ||||
| 29. Round | 13/04/2013 | FC St. Pauli | - | TSV 1860 München | 3:1 | ||||
| 30. Round | 19/04/2013 | VfL Bochum | - | FC St. Pauli | 3:0 | ||||
| 31. Round | 28/04/2013 | FC St. Pauli | - | Hertha BSC | 2:3 |  |
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| 32. Round | 05/05/2013 | MSV Duisburg | - | FC St. Pauli | 0:0 | ||||
| 33. Round | 12/05/2013 | FC St. Pauli | - | Eintracht Braunschweig | 5:1 | ||||
| 34. Round | 19/05/2013 | 1. FC Kaiserslautern | - | FC St. Pauli | 1:2 |
Germany