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| 25/09/2012 | 14:30 | JK Nõmme Kalju | - | FC Levadia | 4:3 aet | |
| 10/10/2012 | 14:00 | Türi Ganvix JK | - | FC Velldoris | 8:1 | |
| 14:00 | Tamme Auto Kiviõli | - | JK Sillamäe Kalev | 0:1 | ||
| 14:00 | Pärnu Linnameeskond | - | Võru JK | 4:2 | ||
| 16:45 | FC Infonet | - | JK Tammeka | 2:4 pso | ||
| 13/10/2012 | 17:00 | Tartu Quattromed | - | JK Narva Trans | 1:7 | |
| 24/10/2012 | 13:00 | FC Viljandi | - | FC Flora II | 3:1 (1:0) | |
| 13:30 | FC Elva | - | FC Flora | 0:2 (0:1) |
