| 1. Round | 27/08/2016 | Borussia Dortmund | - | 1. FSV Mainz 05 | 2:1 |  |
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| 2. Round | 11/09/2016 | 1. FSV Mainz 05 | - | 1899 Hoffenheim | 4:4 | ||||
| 3. Round | 18/09/2016 | FC Augsburg | - | 1. FSV Mainz 05 | 1:3 | |
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| 6. Round | 02/10/2016 | VfL Wolfsburg | - | 1. FSV Mainz 05 | 0:0 | ||||
| 7. Round | 16/10/2016 | 1. FSV Mainz 05 | - | SV Darmstadt 98 | 2:1 | ||||
| 8. Round | 23/10/2016 | FC Schalke 04 | - | 1. FSV Mainz 05 | 3:0 | ||||
| 10. Round | 06/11/2016 | RB Leipzig | - | 1. FSV Mainz 05 | 3:1 | ||||
| 11. Round | 19/11/2016 | 1. FSV Mainz 05 | - | SC Freiburg | 4:2 |  |
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| 12. Round | 27/11/2016 | Hertha BSC | - | 1. FSV Mainz 05 | 2:1 | ||||
| 13. Round | 02/12/2016 | 1. FSV Mainz 05 | - | Bayern München | 1:3 | ||||
| 14. Round | 11/12/2016 | Bor. Mönchengladbach | - | 1. FSV Mainz 05 | 1:0 | ||||
| 15. Round | 17/12/2016 | 1. FSV Mainz 05 | - | Hamburger SV | 3:1 | ||||
| 16. Round | 20/12/2016 | Eintracht Frankfurt | - | 1. FSV Mainz 05 | 3:0 | ||||
| 29. Round | 15/04/2017 | 1. FSV Mainz 05 | - | Hertha BSC | 1:0 | ||||
| 30. Round | 22/04/2017 | Bayern München | - | 1. FSV Mainz 05 | 2:2 | |
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| 31. Round | 29/04/2017 | 1. FSV Mainz 05 | - | Bor. Mönchengladbach | 1:2 |
Austria