| 6. Round | 25/08/2012 | Preußen Münster | - | 1. FC Heidenheim 1846 | 1:1 |  |
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| 7. Round | 28/08/2012 | 1. FC Heidenheim 1846 | - | Chemnitzer FC | 3:2 | ||||
| 8. Round | 02/09/2012 | SV Darmstadt 98 | - | 1. FC Heidenheim 1846 | 0:2 | ||||
| 9. Round | 16/09/2012 | 1. FC Heidenheim 1846 | - | Hansa Rostock | 1:2 | ||||
| 18. Round | 16/11/2012 | 1. FC Heidenheim 1846 | - | 1. FC Saarbrücken | 3:0 |  |
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| 19. Round | 24/11/2012 | Kickers Offenbach | - | 1. FC Heidenheim 1846 | 0:1 | ||||
| 20. Round | 01/12/2012 | Karlsruher SC | - | 1. FC Heidenheim 1846 | 5:2 | ||||
| 22. Round | 15/12/2012 | Stuttgarter Kickers | - | 1. FC Heidenheim 1846 | 0:2 | |
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| 24. Round | 02/02/2013 | SV Babelsberg 03 | - | 1. FC Heidenheim 1846 | 2:4 | ||||
| 25. Round | 09/02/2013 | 1. FC Heidenheim 1846 | - | Preußen Münster | 3:1 |
Germany