| 23. Round | 17/03/2000 | FC St. Pauli | - | Waldhof Mannheim | 1:1 | ||||
| 24. Round | 24/03/2000 | Kickers Offenbach | - | FC St. Pauli | 0:1 |  |
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| 25. Round | 02/04/2000 | FC St. Pauli | - | Fortuna Köln | 0:0 | ||||
| 31. Round | 12/05/2000 | FC St. Pauli | - | Alemannia Aachen | 2:1 | ||||
| 33. Round | 21/05/2000 | 1. FC Köln | - | FC St. Pauli | 6:3 |
Poland