| 20. Round | 04/02/2007 | 1. FC Köln | - | FC Carl Zeiss Jena | 1:0 | ||||
| 21. Round | 11/02/2007 | FC Carl Zeiss Jena | - | Rot-Weiss Essen | 2:0 |  |
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| 22. Round | 18/02/2007 | SC Paderborn 07 | - | FC Carl Zeiss Jena | 0:1 | ||||
| 23. Round | 23/02/2007 | FC Carl Zeiss Jena | - | TSV 1860 München | 3:1 | |
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| 24. Round | 02/03/2007 | SpVgg Unterhaching | - | FC Carl Zeiss Jena | 2:0 | ||||
| 25. Round | 11/03/2007 | FC Carl Zeiss Jena | - | Karlsruher SC | 1:3 | ||||
| 26. Round | 16/03/2007 | TuS Koblenz | - | FC Carl Zeiss Jena | 0:0 | ||||
| 27. Round | 30/03/2007 | FC Carl Zeiss Jena | - | Hansa Rostock | 1:2 | |
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| 28. Round | 08/04/2007 | SpVgg Greuther Fürth | - | FC Carl Zeiss Jena | 2:0 |  |
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| 33. Round | 13/05/2007 | FC Carl Zeiss Jena | - | 1. FC Kaiserslautern | 1:1 | |
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Georgia