Manchester City midfielder Yaya Toure said he was subjected to racist chanting during his team’s 2-1 win in Moscow on Wednesday.
The European governing body says the case will be dealt with by its disciplinary board on 30 October.
CSKA Moscow considers the racism allegations to be “unfounded”.
Manchester City said on Thursday that they had submitted a formal written complaint to UEFA, which is also looking into the setting off of fireworks by home supporters during the match in the Russian capital.
In May, UEFA announced that in the case of racist incidents involving spectators, a partial stadium closure would be applied for the first offence and a full stadium closure for a second, coupled with a fine of 50,000 euros.
CSKA’s next home game in the Champions League is against Bayern Munich on November 27, before which they visit Manchester City on November 5.
Ivory Coast international Yaya Toure said he was “furious” and reported the chants to the referee during the game and afterwards.
But CSKA are “surprised and disappointed” by Yaya Toure’s claims.
A club statement read: “Having carefully studied the video of the game, we found no racist insults from fans of CSKA.”
Lord Ouseley, chairman of anti-discrimination body Kick It Out, said the latest incident would “test” Uefa’s new sanctions.
He added referee Ovidiu Hategan should not officiate again after failing to follow protocol when Toure reported the incidents to him.
Under guidelines issued by UEFA in 2009, referees have the power to tackle racist chanting from supporters in a number of ways.
As a first step, they can stop a match and ask for warnings to be made over the public address system.
The second step is to suspend a match for a short time. If the abuse continues, a match can be abandoned.
Romanian official Ovidiu Hategan, a FIFA referee since 2008, was also in charge when Lazio fans were found guilty of racist behavior towards Tottenham players in the Europa League last season.
FIFPro, the global union for professional footballers, is “disappointed” match officials failed to act.
Sir Ouseley said if players are not adequately protected, more could walk off the pitch during a game, as former AC Milan player Kevin Prince-Boateng did during a friendly last season.
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