| 22. Round | 21/01/2012 | FC Carl Zeiss Jena | - | 1. FC Saarbrücken | 1:1 | ||||
| 26. Round | 22/02/2012 | FC Carl Zeiss Jena | - | SpVgg Unterhaching | 2:0 | ||||
| 27. Round | 25/02/2012 | Chemnitzer FC | - | FC Carl Zeiss Jena | 1:1 | ||||
| 24. Round | 28/02/2012 | FC Carl Zeiss Jena | - | 1. FC Heidenheim 1846 | 0:0 |  |
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| 30. Round | 17/03/2012 | SV Babelsberg 03 | - | FC Carl Zeiss Jena | 0:0 |  |
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| 25. Round | 20/03/2012 | Kickers Offenbach | - | FC Carl Zeiss Jena | 1:1 | ||||
| 31. Round | 24/03/2012 | FC Carl Zeiss Jena | - | Werder Bremen II | 3:1 |  |
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| 23. Round | 27/03/2012 | Preußen Münster | - | FC Carl Zeiss Jena | 1:0 | ||||
| 32. Round | 01/04/2012 | VfB Stuttgart II | - | FC Carl Zeiss Jena | 3:0 | ||||
| 33. Round | 07/04/2012 | FC Carl Zeiss Jena | - | VfL Osnabrück | 2:0 | |
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| 34. Round | 10/04/2012 | VfR Aalen | - | FC Carl Zeiss Jena | 4:1 | |
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| 35. Round | 14/04/2012 | FC Carl Zeiss Jena | - | SV Darmstadt 98 | 2:1 | ||||
| 36. Round | 21/04/2012 | Arminia Bielefeld | - | FC Carl Zeiss Jena | 2:1 | ||||
| 37. Round | 28/04/2012 | FC Carl Zeiss Jena | - | SV Wehen Wiesbaden | 1:0 | ||||
| 38. Round | 05/05/2012 | Jahn Regensburg | - | FC Carl Zeiss Jena | 1:1 | |
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Germany
Montenegro