The visitors could easily have extended their lead in the 14th minute when Akinfeev failed to collect a volley from the left and Daniel Kolar was allowed a header that flew wide of the right post. Two minutes later, Bakos beat Akinfeev in a one-on-one, but Pontus Wernbloom cleared the ball in front of an open goal.
CSKA equalized with its first scoring chance, courtesy of Tosic, who hit the target with a low left-foot shot that took a slight deflection off Raytoral in the 19th.
It was CSKA's first goal in five matches.
Keisuke Honda then put CSKA 2-1 up just 10 minutes later, beating Matus Kozacik in a one-on-one after collecting Tosic's pass.
Ahmed Musa hit the right post of the visitors' goal in the 49th as the Russian champion continued to dominate the game.
CSKA increased its lead when Reznik scored an own goal with a backpass to the keeper, who failed to stop the ball with his right foot. Bakos then headed home the Czech side's second goal in injury time.
The match was originally due to be played at Arena Khimki in Moscow's suburbs, but heavy rains in the region in recent weeks ruined the pitch. UEFA representatives picked Petrovsky stadium in St. Petersburg as a replacement.
