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| 03.04.2009 | 17:00 | FK Khimki | - | FK Rostov | 0:1 (0:0) | |
| 04.04.2009 | 12:00 | Terek Grozny | - | Dinamo Moskva | 1:0 (1:0) | |
| 14:30 | Rubin Kazan | - | FK Moskva | 0:0 (0:0) | ||
| 17:00 | FK Saturn | - | Kuban Krasnodar (1928-2018) | 2:1 (1:1) | ||
| 05.04.2009 | 09:45 | FK Tom Tomsk | - | Zenit St. Petersburg | 0:3 (0:0) | |
| 12:00 | Lokomotiv Moskva | - | Krylia Sovetov | 2:1 (0:1) | ||
| 14:30 | FK Amkar Perm | - | CSKA Moskva | 0:0 (0:0) | ||
| 17:00 | Spartak Moskva | - | Spartak Nalchik | 2:0 (1:0) |
| » Classement | équipe recevante | à l'extérieur | Premier tour | Second tour |
| # | Équipe | M. | G. | N. | P. | Buts | Diff. | Pts. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Zenit St. Petersburg | 3 | 2 | 1 | 0 | 6:2 | 4 | 7 |
| 2 |
|
Terek Grozny | 3 | 2 | 1 | 0 | 2:0 | 2 | 7 |
| 3 |
|
Dinamo Moskva | 3 | 2 | 0 | 1 | 4:3 | 1 | 6 |
| 4 |
|
Krylia Sovetov | 3 | 2 | 0 | 1 | 3:2 | 1 | 6 |
| 5 |
|
Rubin Kazan | 3 | 1 | 2 | 0 | 3:0 | 3 | 5 |
| 6 |
|
Lokomotiv Moskva | 3 | 1 | 2 | 0 | 4:3 | 1 | 5 |
| 7 |
|
FK Rostov | 3 | 1 | 2 | 0 | 2:1 | 1 | 5 |
| 8 |
|
CSKA Moskva | 3 | 1 | 1 | 1 | 3:1 | 2 | 4 |
| 9 |
|
Spartak Moskva | 3 | 1 | 1 | 1 | 3:2 | 1 | 4 |
| 10 |
|
FK Saturn | 3 | 1 | 0 | 2 | 3:6 | -3 | 3 |
| 11 |
|
Kuban Krasnodar (1928-2018) | 3 | 1 | 0 | 2 | 2:5 | -3 | 3 |
| 12 |
|
FK Tom Tomsk | 3 | 1 | 0 | 2 | 1:4 | -3 | 3 |
| 13 |
|
FK Moskva | 3 | 0 | 2 | 1 | 0:1 | -1 | 2 |
| 14 |
|
FK Amkar Perm | 3 | 0 | 2 | 1 | 0:1 | -1 | 2 |
| 15 |
|
FK Khimki | 3 | 0 | 1 | 2 | 3:5 | -2 | 1 |
| 16 |
|
Spartak Nalchik | 3 | 0 | 1 | 2 | 0:3 | -3 | 1 |
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| Europa League | |
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