Villa boss Martin O'Neill had opted to rest a host of first-team regulars for the trip to the Russian capital, with Barry Bannan handed just a second senior appearance.
With the tie evenly poised at 1-1, Craig Gardner flashed an early shot over the top, before Vassily Berezutsky fired over the top following a Yuri Zhirkov, corner.
Fourteen minutes in Nathan Delfouneso forced a save from home keeper Igor Akinfeev, but neither side could fashion a clear-cut opening.
The game then became bogged down in midfield, before the home side pushed on in the final 15 minutes of the half.
Berezutsky headed wide from a Milos Krasic corner, before Villa keeper Brad Guzan was forced to make saves from Vagner Lover, Krasic and Alan Dzagoyev. Love shot wide to end the half, with the tie still in the balance.
CSKA continued to dominate as the second half got underway, with Krasic shooting narrowly wide of target, before Dzagoyev failed to test Guzan with an effort from the edge of the area.
On the hour mark the home side finally took the lead on the night and on aggregate, as Dzagoyev played a free-kick across the Villa area and Zhirkov was in the right place to place the ball past Guzan.
Soon after, Guzan did well to block another effort from the impressive Zhirkov, as CSKA pushed for a killer second goal.
Thirteen minutes from time Krasic's fierce shot again extended Guzan, as Villa started to buckle under heavy pressure.
They were put out of their misery deep into stoppage time as Krasic set up Love and he beat Guzan with ease to make the final score 2-0.