Midfielder Yaya Toure complained of racist abuse after the match and called on UEFA to take action against the Russian side.
CSKA Moscow has subsequently denied claims of racial abuse telling Sky Sports News: "There is no subject to discuss. Nothing special happened."
However, UEFA has now confirmed that it has launched disciplinary proceedings into the behavior of the club's fans, with the case to be heard at the end of the month.
"Disciplinary proceedings have been opened against PFC CSKA Moskva for racist behavior 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," a statement reads.
"The case will be dealt with by the UEFA Control and Disciplinary Body on 30 October."