| 3. Round | 31/08/1958 | VfV Hildesheim | - | FC St. Pauli | 2:2 |  |
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| 4. Round | 07/09/1958 | FC St. Pauli | - | TuS Bremerhaven 93 | 3:3 | ||||
| 5. Round | 14/09/1958 | Hannover 96 | - | FC St. Pauli | 0:0 | ||||
| 6. Round | 28/09/1958 | FC St. Pauli | - | Hamburger SV | 0:8 | ||||
| 7. Round | 05/10/1958 | FC St. Pauli | - | Concordia Hamburg | 3:1 | ||||
| 8. Round | 12/10/1958 | VfL Osnabrück | - | FC St. Pauli | 1:0 | ||||
| 9. Round | 19/10/1958 | FC St. Pauli | - | 1. FC Phönix Lübeck | 1:0 | ||||
| 23. Round | 15/02/1959 | 1. FC Phönix Lübeck | - | FC St. Pauli | 3:3 | |
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| 26. Round | 15/03/1959 | FC St. Pauli | - | Hannover 96 | 2:2 | ||||
| 28. Round | 30/03/1959 | FC St. Pauli | - | VfL Osnabrück | 5:1 | ||||
| 28. Round | 05/04/1959 | VfL Wolfsburg | - | FC St. Pauli | 2:3 | |
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| 24. Round | 12/04/1959 | FC St. Pauli | - | VfV Hildesheim | 1:1 | ||||
| 29. Round | 19/04/1959 | FC St. Pauli | - | Holstein Kiel | 2:1 | ||||
| 30. Round | 26/04/1959 | TuS Bremerhaven 93 | - | FC St. Pauli | 1:4 |
Germany