UEFA also said that their venue director for CSKA's Arena Khimka has been "relieved of his duties" for failing to stop play and issue a warning over the public address system as laid down in UEFA guidelines. The referee was absolved of any blame.
UEFA's disciplinary panel ordered the closure of sector D of the Arena Khimki for the match against Bayern Munich in Moscow on Nov. 27 after Ivorian midfielder Toure said he was racially insulted during City's 2-1 win in the Champions League.
Toure, who added that black players could boycott the 2018 World Cup in Russia if the country does not tackle the issue, reported the incidents to the referee during the game but no action was taken.
This was despite UEFA guidelines issued in 2009 that call for play to be stopped and a warning to be broadcast over the public address system. Ultimately, officials have the power to call off the game if the abuse continues.
UEFA said it had completed an investigation ordered by president Michel Platini into why they were not followed.
"In the 54th minute of the Group D fixture, the Romanian referee Ovidiu Haegan stopped the game to award a free kick and give a yellow card to a CSKA player," UEFA said.
"While play was stopped, the referee was approached by City captain Yaya Toure, who complained that home fans were directing racist chants towards him.
"The referee and the additional assistant referee standing on that side of the field witnessed the inappropriate behaviour of a small number of fans.
"The referee immediately asked the fourth official to request an announcement to be made to the public.
"The venue director (the UEFA officer in charge of football operations), who had not heard the chanting himself, did not activate the procedure. As the chanting had ceased, the referee decided to resume the game with the free-kick.
"The conclusion of the investigation is therefore that the referee had correctly triggered the first step of the procedure by requesting the stadium announcement.
"The venue director acted inappropriately, though in good faith, so causing the failure in the activation of the first step of the standard procedure, as decided by the referee.
"The UEFA venue director at the Arena Khimki has been relieved of his duties."
CSKA had said they were "surprised and disappointed" by Toure's allegations of racism.
Piara Power, executive director of Football Against Racism in Europe (FARE), said on Twitter: "UEFA CSKA sanction is a clear signal. Racism and other forms of discriminatory abuse will be punished. Education is only answer long term."
Toure, who speaks Russian after spending two years playing in Ukraine for Metallurg Donetsk, said the abuse he experienced in Moscow was worse than anything he had encountered in Ukraine.
Under regulations introduced by UEFA this season to combat racism, a partial stadium closure is the minimum sanction for racist behaviour.
A second offence by supporters will lead to a full stadium closure for the following European match and a 50,000 euro fine. Racist behaviour by players or officials leads to a minimum 10-match ban.
Lech Poznan, Piast Gliwice and Dinamo Zagreb have been forced into partial closures this season for racist behaviour by supporters. Honved had to play two home games behind closed doors.
Legia Warsaw were ordered to play one home match behind closed doors in the Europa League.