Edin Dzeko had put the German champions ahead against the run of play midway through the first half before Czech striker Tomas Necid and Serbian winger Milos Krasic struck eight minutes apart early in the second half to give the Russians the points.
The win moved CSKA level with second-placed Wolfsburg on seven points with the last round of matches to come.
But the Germans, who needed only a draw in Moscow to join English champions Manchester United in the last 16, still have the edge over CSKA after beating them 3-1 in the first game.
CSKA coach Leonid Slutsky had mixed feelings about the outcome. "I'm satisfied with the win but a little disappointed because I was hoping for a bigger victory," he told Russian television NTV.
"Still, the whole team showed a lot of courage to pull off this win after falling behind early in the game."
Obafemi Martins sent Dzeko through and the Bosnian striker beat the offside trap to shoot past CSKA keeper Igor Akinfeyev from close range in the 19th minute.
SPEEDY KRASIC
Krasic could have levelled just a few minutes later but missed the target after dribbling past several Wolfsburg defenders.
CSKA defender Alexei Berezutsky then wasted another great chance, shooting straight at Wolfsburg keeper Diego Benaglio from six metres following a corner. Benaglio also made a fine save to deny Pavel Mamayev early in the second half.
Necid finally beat Benaglio with a powerful header from close range in the 58th minute after pin-point cross from Yevgeny Aldonin.
Krasic, who tormented the German defence with great solo runs on the artificial Luzhniki turf throughout the game, then fired the hosts ahead with a 30-metre blast into the top corner.
At the other end, Dzeko had the ball in the CSKA goal for a second time shortly after the re-start but this time he was ruled offside.
Wolfsburg, who were missing their top scorer Brazilian Grafite through suspension, pressed forward late in the game and Marcel Schaefer came close with an equaliser only for Akinfeyev to push the ball over the bar and preserve the win.
In the final group games on December 9, Wolfsburg host Manchester United, who have already qualified, while CSKA travel to Istanbul to play Besiktas.
