Montenegro's FA (FSCG) is also being investigated for "holding a match that did not get played in full", UEFA said in a statement. The match was goalless when it was abandoned.
The game was first delayed by 33 minutes when Russia goalkeeper Igor Akinfeev was hit on the head by a flare thrown from the Montenegro section of the ground soon after kickoff.
He had to come off and was taken to hospital with burns.
Midway through the second half a scuffle ensued between players near the touchline and Russia midfielder Dmitri Kombarov was hit by a missile prompting the referee to abandon the game.
The Football Union of Russia (RFS) has lodged a protest with UEFA and wants to be awarded the points. Third-placed Russia and Montenegro in fourth are level on five points from four matches.
(Writing by Ken Ferris, editing by Pritha Sarkar)
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