| 20. Round | 01/02/2009 | Panionios GSS | - | Panthrakikos | 3:0 | ||||
| 21. Round | 07/02/2009 | Aris Saloniki | - | Panionios GSS | 1:0 |  |
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| 22. Round | 14/02/2009 | Panionios GSS | - | Ergotelis | 0:0 | ||||
| 23. Round | 21/02/2009 | Panathinaikos | - | Panionios GSS | 2:1 | |
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| 25. Round | 07/03/2009 | Iraklis Saloniki | - | Panionios GSS | 2:1 | ||||
| 26. Round | 15/03/2009 | Levadiakos | - | Panionios GSS | 1:1 | ||||
| 27. Round | 22/03/2009 | Panionios GSS | - | Olympiakos Piraeus | 2:3 | ||||
| 28. Round | 05/04/2009 | AE Lárissa | - | Panionios GSS | 0:0 | ||||
| 29. Round | 12/04/2009 | Panionios GSS | - | Thrasyvoulos Fylis | 4:1 |
Czech Republic