The pair were both dismissed in the second half as City struggled to get back into a Group E contest they were anxious to win to revive their campaign.
Seydou Doumbia was again City's nemesis, following up his influential role in last month's 2-2 draw in Moscow with both CSKA goals
His Ivory Coast team-mate Toure had cancelled out his first with a superb free-kick - but City again lacked spark in Europe's elite competition.
The result left them with just two points from four games and bottom of the group.
City could have had two penalties in the dying minutes but Sergio Aguero, denied two spot-kicks in Sunday's Manchester derby, was twice refused again.
There were plenty of other issues surrounding the game, with no CSKA fans having officially been sold tickets but a number making themselves heard.
CSKA were also without winger Zoran Tosic amid reports he had not obtained the correct visa.
City's night could hardly have begun in worse fashion as Gael Clichy was penalised for handball and Bebras Natcho swung in a free-kick for Doumbia to head in after two minutes.
The ground was stunned into silence and was quieter than the Khimki Arena had been when the sides met a fortnight ago in a game that was officially played behind closed doors.
Prior to kick-off many City fans had made themselves heard as they booed the Champions League anthem in protest at what they believe has been unfair treatment from UEFA with regards to the game in Moscow.
But the supporters' attempts to follow that by generating an atmosphere to inspire City quickly fell flat as a result of Doumbia's firm header.
City needed something else to rouse them and Toure provided it with an exquisite free-kick
Stevan Jovetic was bundled over on the edge of the area and the Ivorian stepped up to curl a shot into the top corner and level the scores.
But still the crowd remained subdued and City seemed to have little energy to feed off.
CSKA did not have the majority of possession but they made better use of it and Alan Dzagoev released Doumbia with a defence-splitting pass - but he drove wide.
City pushed back and Aguero was twice denied by Russia goalkeeper Igor Akinfeev.
The atmosphere cranked up a little as it became apparent some CSKA fans were being ejected and tempers could have flared when Pontus Wernbloom took out Toure with a poor challenge.
Still the spark was lacking and City were caught out again when Clichy gave the ball away and Natcho teed up Doumbia again after 34 minutes
Again his finish was clinical as he clipped the ball inside Joe Hart's near post.
Manuel Pellegrini made a double change at half-time to try to change the course of the game with Samir Nasri and Fernandinho entering for Jesus Navas and Jovetic.
City began to take greater control of the game but still needed Hart to be alert to keep out an Ahmed Musa effort.
James Milner began to have a greater influence and Toure went down in the area after a powerful run but was denied a penalty.
Milner almost created a chance for Aguero with a dangerous cross but the Argentinian failed to connect by inches
Milner then went close himself after finding space in front of goal but Akinfeev saved with his feet.
Pablo Zabaleta then fired wide and Aguero had another attempt blocked but City's problems reached serious proportions as Fernandinho was dismissed.
The Brazilian, booked minutes earlier for a foul on Dzagoev, was penalised again for blocking Musa on the edge of the area
It seemed accidental but referee Tasos Sidiropoulos took a dim view and showed a second yellow - and the red.
City were slow to respond and substitute Edin Dzeko could not make the most of an opportunity in the box.
There was further controversy as Aguero was felled outside the area by a combination of CSKA players
Wernbloom might easily have received a second booking but only Sergei Ignashevich was cautioned.
City crumbled and their frustration was evident in Toure's sending off eight minutes from time
Toure's run was blocked by Roman Eremenko but the City midfielder raised his hands to shove him away
He had already been booked but Sidiropoulos showed a straight red.
City were almost caught out late on as Hart tipped over a curling effort from Musa.
Aguero twice looked to have been fouled in the box as he fought to the end but Sidiropoulos gave nothing and was surrounded by City players after blowing the final whistle.
Source : PA
Source: PA