Arjen Robben's first goal for Chelsea sealed qualification for the Champions League knockout stage.
The £12m signing from PSV Eindhoven finished off a glorious link with Damien Duff to score in style from 12 yards after 24 minutes.
CSKA applied pressure after the break, but Vagner Love fired a penalty over the bar after Glen Johnson fouled Yuri Zhirkov seconds after half-time.
It left Chelsea still with a 100% record of four wins in the group phase.
Robben posted the warning signals for CSKA in the 23rd minute when he cut dangerously inside and fired narrowly off target.
He made no mistake a minute later when he set the seal on a superb move involving Duff to put Chelsea in front.
The pair showed perfect understanding and imagination as Duff set up Robben with a back-heel that allowed the Dutch winger to ease past a defender before placing a precision left-foot finish past Igor Akinfeev.
Chelsea were moving smoothly through the gears and it needed a desperate goal-line clearance from Sergei Semak to deny Eidur Gudjohnsen after more good work by Robben.
CSKA were getting little encouragement from Chelsea's rearguard, but Wagner Love almost equalised when he forced a fine diving save out of Petr Cech six minutes before half-ttime.
Chelsea were almost punished for a lapse in concentration seconds after the re-start when referee Massimo de Santis pointed to the spot after Johnson upended Zhirkov.
But Chelsea were handed a reprieve as Wagner Love lashed the penalty high over the top.
CSKA were encouraged and it needed another fine block from Cech to save Jiri Jarosik's 20-yard drive.
Chelsea were suddenly under pressure, and Mourinho made a change after 65 minutes, replacing Scott Parker with Tiago.
And Chelsea sent on Mateja Kezman for Gudjohnsen two minutes later.
Kezman's first involvement was to pick a yellow card for a crashing challenge on goalkeeper Akinfeev.
Chelsea almost finished with a flourish as Frank Lampard saw a close-range shot saved by Akinfeev.
CSKA were better after the break, but Chelsea survived in relative comfort to complete an impressive passage into the next stage of the competition.
CSKA Moscow: Akinfeev, Semberas, Ignashevich, Semak (Olic 70),
Berezoutski, Gusev, Vagner Love (Kirichenko 82), Krasic (Aldonin 46), Zhirkov, Jarosik, Rahimic.
Subs Not Used: Mandrykin, Ferreyra, Laizans, Shershun.
Booked: Olic, Semberas.
Chelsea: Cech, Johnson, Terry, Ricardo Carvalho, Gallas (Paulo Ferreira 54), Duff, Parker (Tiago 65), Lampard, Makelele, Robben, Gudjohnsen (Kezman 68).
Subs Not Used: Cudicini, Babayaro, Cole, Huth.
Booked: Johnson, Kezman.
Goals: Robben 24.
Ref: Massimo De Santis (Italy).