| 6. Round | 25/08/2012 | Preußen Münster | - | 1. FC Heidenheim 1846 | 1:1 | ||||
| 10. Round | 21/09/2012 | SV Wehen Wiesbaden | - | 1. FC Heidenheim 1846 | 1:1 |  |
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| 11. Round | 26/09/2012 | Wacker Burghausen | - | 1. FC Heidenheim 1846 | 4:1 | ||||
| 14. Round | 20/10/2012 | 1. FC Heidenheim 1846 | - | VfL Osnabrück | 1:3 | ||||
| 18. Round | 16/11/2012 | 1. FC Heidenheim 1846 | - | 1. FC Saarbrücken | 3:0 | ||||
| 19. Round | 24/11/2012 | Kickers Offenbach | - | 1. FC Heidenheim 1846 | 0:1 | |
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| 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 | ||||
| 24. Round | 02/02/2013 | SV Babelsberg 03 | - | 1. FC Heidenheim 1846 | 2:4 | ||||
| 27. Round | 23/02/2013 | 1. FC Heidenheim 1846 | - | SV Darmstadt 98 | 3:0 | |
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| 28. Round | 02/03/2013 | Hansa Rostock | - | 1. FC Heidenheim 1846 | 0:2 | ||||
| 29. Round | 09/03/2013 | 1. FC Heidenheim 1846 | - | SV Wehen Wiesbaden | 2:2 | ||||
| 30. Round | 16/03/2013 | 1. FC Heidenheim 1846 | - | Wacker Burghausen | 2:1 | ||||
| 35. Round | 27/04/2013 | Alemannia Aachen | - | 1. FC Heidenheim 1846 | 1:2 |
Germany