| 18. Round | 05/02/2000 | FC Carl Zeiss Jena | - | Hertha BSC II | 3:1 |  |
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| 19. Round | 12/02/2000 | VfL Halle 96 | - | FC Carl Zeiss Jena | 0:6 | ||||
| 20. Round | 19/02/2000 | FC Carl Zeiss Jena | - | Dynamo Dresden | 3:0 | ||||
| 21. Round | 06/04/2000 | Sachsen Leipzig | - | FC Carl Zeiss Jena | 0:1 | ||||
| 27. Round | 11/04/2000 | FC Carl Zeiss Jena | - | Stahl Eisenhüttenstadt | 2:0 | ||||
| 28. Round | 15/04/2000 | BFC Dynamo | - | FC Carl Zeiss Jena | 0:2 | ||||
| 29. Round | 22/04/2000 | FC Carl Zeiss Jena | - | Dresdner SC | 0:0 | ||||
| 30. Round | 29/04/2000 | VfB Leipzig | - | FC Carl Zeiss Jena | 1:2 | |
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| 24. Round | 02/05/2000 | FC Carl Zeiss Jena | - | Erzgebirge Aue | 2:1 | ||||
| 31. Round | 05/05/2000 | FC Carl Zeiss Jena | - | TeBe Berlin II | 2:1 | ||||
| 32. Round | 09/05/2000 | 1. FC Magdeburg | - | FC Carl Zeiss Jena | 2:3 | ||||
| 33. Round | 13/05/2000 | FC Carl Zeiss Jena | - | FSV Zwickau | 2:1 | ||||
| 34. Round | 20/05/2000 | Rot-Weiß Erfurt | - | FC Carl Zeiss Jena | 2:0 |
Germany