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| 01/09/2009 | 16:00 | Põlva Lootos | - | FC Kuressaare | 2:5 | |
| 02/09/2009 | 16:00 | JK Tallinna Kalev | - | Koeru SK | 8:1 | |
| 16:00 | EMÜ SK | - | FC Flora II | 0:5 | ||
| 16:00 | Ajax Lasnamäe | - | Lootus Kohtla-Järve | 0:3 | ||
| 16:00 | JK Narva Trans | - | FC Haiba | 13:0 | ||
| 16:45 | JK Nõmme Kalju | - | Tulevik Viljandi II | 5:0 | ||
| 08/09/2009 | 15:30 | JK Sillamäe Kalev II | - | FC Levadia | 0:5 | |
| 15:30 | Warrior Valga | - | JK Nõmme Kalju II | 1:0 | ||
| 16:45 | Tallinna Olympic | - | JK Tammeka | 2:3 | ||
| 09/09/2009 | 15:30 | Jõhvi JK Orbiit | - | Türi Ganvix JK | 1:3 | |
| 16:00 | FC Atletik | - | Eston Villa | 2:1 aet | ||
| 16/09/2009 | 15:00 | JK Sillamäe Kalev | - | Tulevik Viljandi | 3:1 aet | |
| 30/09/2009 | 17:00 | Nõmme United | - | Tamme Auto Kiviõli | 5:2 | |
| 17:30 | JK Piraaja Tallinn | - | Tabasalu JK | 5:3 | ||
| 06/10/2009 | 16:45 | FC Flora | - | FC Otepää | 4:1 |
