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| 15.09.2012 | 13:00 | FC Levadia | - | JK Nõmme Kalju | 0:1 (0:0) | |
| 16:00 | FC Viljandi | - | JK Tallinna Kalev | 2:1 (1:1) | ||
| 16:00 | FC Kuressaare | - | Paide Linnameeskond | 1:1 (0:0) | ||
| 16:00 | JK Tammeka | - | JK Narva Trans | 2:1 (2:1) | ||
| 18:30 | FC Flora | - | JK Sillamäe Kalev | 4:0 (3:0) |
| # | Mannschaft | Sp. | S. | U. | N. | Tore | Dif. | Pk. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
JK Nõmme Kalju | 28 | 24 | 3 | 1 | 78:9 | 69 | 75 |
| 2 |
|
FC Levadia | 28 | 18 | 8 | 2 | 65:16 | 49 | 62 |
| 3 |
|
FC Flora | 28 | 20 | 2 | 6 | 64:19 | 45 | 62 |
| 4 |
|
JK Narva Trans | 28 | 12 | 5 | 11 | 35:29 | 6 | 41 |
| 5 |
|
JK Sillamäe Kalev | 28 | 10 | 9 | 9 | 33:34 | -1 | 39 |
| 6 |
|
Paide Linnameeskond | 28 | 9 | 6 | 13 | 25:38 | -13 | 33 |
| 7 |
|
FC Viljandi | 28 | 6 | 7 | 15 | 26:53 | -27 | 25 |
| 8 |
|
FC Kuressaare | 28 | 4 | 9 | 15 | 21:61 | -40 | 21 |
| 9 |
|
JK Tallinna Kalev | 28 | 4 | 7 | 17 | 22:66 | -44 | 19 |
| 10 |
|
JK Tammeka | 28 | 2 | 6 | 20 | 17:61 | -44 | 12 |
| Champions League Quali. | |
| Europa League Quali. | |
| Relegation | |
| Abstieg |
