| 1. Round | 15/08/2008 | FC St. Pauli | - | VfL Osnabrück | 2:2 |  |
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| 3. Round | 31/08/2008 | FC St. Pauli | - | Rot-Weiß Oberhausen | 4:1 | ||||
| 4. Round | 12/09/2008 | 1. FC Kaiserslautern | - | FC St. Pauli | 4:1 |  |
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| 7. Round | 05/10/2008 | FC St. Pauli | - | Alemannia Aachen | 3:2 | ||||
| 8. Round | 19/10/2008 | FC Augsburg | - | FC St. Pauli | 3:2 | ||||
| 18. Round | 30/01/2009 | VfL Osnabrück | - | FC St. Pauli | 2:2 |  |
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| 21. Round | 23/02/2009 | FC St. Pauli | - | 1. FC Kaiserslautern | 2:0 |
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