| 10. Round | 31/08/2012 | SV Heimstetten | - | FC Augsburg II | 1:1 |  |
|||
| 11. Round | 08/09/2012 | FC Augsburg II | - | TSV 1860 München II | 0:1 |  |
|||
| 12. Round | 14/09/2012 | SC Eltersdorf | - | FC Augsburg II | 4:1 | ||||
| 16. Round | 07/10/2012 | 1. FC Nürnberg II | - | FC Augsburg II | 2:0 | ||||
| 15. Round | 17/10/2012 | FC Augsburg II | - | TSV 1860 Rosenheim | 5:0 | |
|||
| 18. Round | 20/10/2012 | VfL Frohnlach | - | FC Augsburg II | 2:2 | ||||
| 19. Round | 27/10/2012 | FC Augsburg II | - | Eintracht Bamberg | 5:2 | ||||
| 20. Round | 02/11/2012 | FC Augsburg II | - | Bayern München II | 2:2 | ||||
| 21. Round | 10/11/2012 | FC Ismaning | - | FC Augsburg II | 1:2 | |
|||
| 22. Round | 17/11/2012 | FC Augsburg II | - | SpVgg Greuther Fürth II | 3:1 | |
|||
| 23. Round | 24/11/2012 | FC Augsburg II | - | Viktoria Aschaffenburg | 5:0 | |
Kosovo