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| 05/10/2016 | 18:00 | JK Tammeka | - | Rumori Calcio | 5:1 (1:0) | |
| 12/10/2016 | 17:00 | FC Kuressaare | - | Raplamaa JK II | 5:0 | |
| 16/10/2016 | 16:00 | EMÜ SK | - | Tulevik Viljandi | 0:5 (0:5) | |
| 18/10/2016 | 16:00 | FC Infonet | - | FC Levadia | 2:1 (0:0) | |
| 19/10/2016 | 16:00 | JK Nõmme Kalju | - | FC Flora | 1:0 (1:0) | |
| 17:00 | FC Infonet II | - | Paide Linnameeskond | 1:4 (0:3) | ||
| 17:00 | FC Flora II | - | Narva United FC | 1:3 (0:1) | ||
| 15/11/2016 | 18:00 | FC Molycorp Silmet | - | JK Tallinna Kalev | 0:11 (0:5) |
