| 1. Round | 17/08/2008 | 1. FC Nürnberg | - | FC Augsburg | 2:1 | ||||
| 2. Round | 24/08/2008 | FC Augsburg | - | Rot Weiss Ahlen | 3:0 | ||||
| 3. Round | 29/08/2008 | MSV Duisburg | - | FC Augsburg | 2:0 |  |
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| 4. Round | 14/09/2008 | FC Augsburg | - | SC Freiburg | 1:3 | ||||
| 18. Round | 30/01/2009 | FC Augsburg | - | 1. FC Nürnberg | 0:0 | |
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| 19. Round | 08/02/2009 | Rot Weiss Ahlen | - | FC Augsburg | 2:1 | |
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| 22. Round | 01/03/2009 | FC Augsburg | - | TuS Koblenz | 0:2 | ||||
| 23. Round | 08/03/2009 | 1. FSV Mainz 05 | - | FC Augsburg | 1:1 | ||||
| 24. Round | 15/03/2009 | FC Augsburg | - | Rot-Weiß Oberhausen | 1:2 | ||||
| 25. Round | 22/03/2009 | FC St. Pauli | - | FC Augsburg | 1:1 | ||||
| 26. Round | 03/04/2009 | FC Augsburg | - | FC Ingolstadt 04 | 1:1 | ||||
| 27. Round | 12/04/2009 | FSV Frankfurt | - | FC Augsburg | 2:1 | ||||
| 28. Round | 17/04/2009 | FC Augsburg | - | VfL Osnabrück | 3:0 | ||||
| 29. Round | 24/04/2009 | SpVgg Greuther Fürth | - | FC Augsburg | 2:1 | |
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| 30. Round | 01/05/2009 | FC Augsburg | - | TSV 1860 München | 3:0 | ||||
| 31. Round | 08/05/2009 | 1. FC Kaiserslautern | - | FC Augsburg | 1:0 | ||||
| 34. Round | 24/05/2009 | Alemannia Aachen | - | FC Augsburg | 4:0 |
Germany