| 1. Round | 12/08/2012 | RB Leipzig | - | 1. FC Union Berlin II | 1:1 | ||||
| 2. Round | 26/08/2012 | 1. FC Union Berlin II | - | Energie Cottbus II | 2:2 | ||||
| 3. Round | 02/09/2012 | FSV Zwickau | - | 1. FC Union Berlin II | 4:0 | ||||
| 4. Round | 14/09/2012 | 1. FC Union Berlin II | - | FC Carl Zeiss Jena | 0:1 | ||||
| 17. Round | 24/03/2013 | Energie Cottbus II | - | 1. FC Union Berlin II | 4:1 |  |
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| 22. Round | 30/03/2013 | TSG Neustrelitz | - | 1. FC Union Berlin II | 0:0 | ||||
| 16. Round | 03/04/2013 | 1. FC Union Berlin II | - | RB Leipzig | 1:2 | ||||
| 26. Round | 27/04/2013 | VfB Auerbach | - | 1. FC Union Berlin II | 2:1 | |
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| 18. Round | 08/05/2013 | 1. FC Union Berlin II | - | FSV Zwickau | 1:3 | ||||
| 28. Round | 11/05/2013 | VFC Plauen | - | 1. FC Union Berlin II | 2:2 | ||||
| 19. Round | 15/05/2013 | FC Carl Zeiss Jena | - | 1. FC Union Berlin II | 1:0 | ||||
| 29. Round | 19/05/2013 | 1. FC Union Berlin II | - | Hertha BSC II | 0:1 | ||||
| 30. Round | 25/05/2013 | Torgelower SV Greif | - | 1. FC Union Berlin II | 0:3 |
Germany