City midfielder Toure, who is from Ivory Coast, complained to the referee that CSKA fans abused him during the English club's 2-1 win in Moscow.
No action was taken at the time, but UEFA have noted the referee's report and have opened disciplinary proceedings against the Russian side for racist behaviour and for setting off fireworks from the stands.
"Disciplinary proceedings have been opened against CSKA Moscow for racist behaviour of their fans (article 14 of the UEFA disciplinary regulations) and for setting off of fireworks (article 16) at last night's UEFA Champions League group stage match in Moscow against Manchester City FC," UEFA said in a statement.
"The case will be dealt with by the UEFA Control and Disciplinary Body on October 30."
UEFA has warned that clubs will no longer escape with just fines if their supporters are guilty of discriminatory behaviour.
CSKA spokesman Michael Sanadze insisted that there is no case to answer, however.
"There is no subject to discuss," Sanadze said. "Nothing special happened.
"There was a lot of noise in the stadium. Nobody else, other than Yaya Toure, heard anything. The only trouble that has come about was because Yaya Toure heard something."
The club, via their official website, added: "In a thorough study of the videotape, we found no racist insults directed at the guests by CSKA fans, and the delegate confirmed this at the end of the match."
It said there were several moments during the match when CSKA were under attack and its fans "tried to pressure the opposing side's players with boos and whistles, regardless of their race."
"In any case, we regret the incident, although we consider accusations of racism to be groundless," it said.
That claim seems to fly in the face of what appeared to happen on the pitch, with Toure and his team-mates protesting to the referee during the game - only to be waved away and told to carry on.
Referee Ovidio Hategan's failure to act on the complaint led Kick It Out chairman Lord Ouseley to call for him to be banned from officiating at future games.
"The referee should not be refereeing again," Ouseley told the BBC."
He failed to do his duty last night and that is a clear issue that UEFA should be dealing with."
Toure himself was evidently deeply hurt by the incident.
"I'm not just disappointed, I'm furious," he said. "I'm very, very disappointed about what those fans have done and I think UEFA has to take action because players with the same colour of skin will always be in the same position.
"For me, as captain, I was wearing an armband which said 'no to racism' and I was totally disappointed.
"Maybe they could ban the stadium, I don't know, for a couple of years or a couple of months.
"It's stupid these people. I don't know, it just happens in football. It's unbelievable. UEFA has to take action to right it otherwise I think they will just continue."
So far this season, UEFA has imposed full stadium bans on three clubs - Dinamo Zagreb of Croatia, Legia Warsaw of Poland and Honved of Hungary - for racist behaviour by their supporters while five other clubs have had partial stadium closures imposed.
They are: Lazio (who were originally handed a full stadium closure but that was reduced on appeal), Polish clubs Lech Poznan and Piast Gliwice, APOEL Nicosia of Cyprus and Croatian outfit HNK Rijeka.
The world players' union FIFPro criticised UEFA, saying their match officials had failed to follow the three-step protocol for dealing with racism in stadiums and which calls for matches to be abandoned in extreme cases.
"We're very disappointed that a clear agreed protocol which is designed to deal with these situations was not implemented," said Bobby Barnes, head of FIFPro's Europe division.
"The player, having done what was asked of him to notify the referee, quite rightly expected that the referee would go speak with the safety officer," said Barnes.
"The (UEFA) protocol agreed is that the safety officer should make a stadium announcement warning the fans that if the chants do not desist that the game will be stopped."
Toure's anger comes at a time when ethnic tension is higher than usual in Moscow.
The stabbing death of an ethnic Russian man was widely blamed on a migrant from mostly Muslim Azerbaijan, touching off a nationalist riot on Oct. 13 - the biggest outbreak of ethnic unrest in the capital in three years.
Putin underlined Kremlin concerns that ethnic or religious tensions could threaten Russia's unity in comments on Tuesday.
He accused foreign rivals of using radical Islam to weaken Russia and deflected any responsibility for ethnic and religious strife, putting the blame partly on local authorities.
In December 2010, several thousand youths rioted just outside the Kremlin, clashing with police and attacking passersby who they took for non-Russians after the killing of an ethnic Russian soccer fan was blamed on a man from the North Caucasus.
A spokeswoman for the Russian Sports Ministry declined to comment and referred questions to the minister, Vitaly Mutko, who could not immediately be reached.
The Russian Soccer Union also declined to comment.