| 23. Round | 26/01/2013 | 1. FC Heidenheim 1846 | - | SpVgg Unterhaching | 2:1 | ||||
| 21. Round | 30/01/2013 | 1. FC Heidenheim 1846 | - | Rot-Weiß Erfurt | 2:1 |  |
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| 25. Round | 09/02/2013 | 1. FC Heidenheim 1846 | - | Preußen Münster | 3:1 |  |
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| 26. Round | 16/02/2013 | Chemnitzer FC | - | 1. FC Heidenheim 1846 | 2:1 | ||||
| 27. Round | 23/02/2013 | 1. FC Heidenheim 1846 | - | SV Darmstadt 98 | 3:0 | ||||
| 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 | ||||
| 32. Round | 06/04/2013 | 1. FC Heidenheim 1846 | - | VfB Stuttgart II | 1:0 | ||||
| 33. Round | 13/04/2013 | VfL Osnabrück | - | 1. FC Heidenheim 1846 | 2:2 | ||||
| 31. Round | 16/04/2013 | Hallescher FC | - | 1. FC Heidenheim 1846 | 0:0 | |
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| 34. Round | 20/04/2013 | 1. FC Heidenheim 1846 | - | Arminia Bielefeld | 3:0 | |
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| 35. Round | 27/04/2013 | Alemannia Aachen | - | 1. FC Heidenheim 1846 | 1:2 | ||||
| 36. Round | 04/05/2013 | 1. FC Heidenheim 1846 | - | Borussia Dortmund II | 2:2 | ||||
| 37. Round | 11/05/2013 | 1. FC Saarbrücken | - | 1. FC Heidenheim 1846 | 1:2 | |
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| 38. Round | 18/05/2013 | 1. FC Heidenheim 1846 | - | Kickers Offenbach | 0:0 |
Germany