It was a defeat that was widely anticipated but Villa's young guns excelled in testing conditions to provide a few positives on a night of disappointment.
Yuri Zhirkov and Vagner Love saw CSKA through 3-1 on aggregate as Martin O'Neill left most of his first team at home.
But Barry Bannan and Marc Albrighton put in hard working, adept shifts to lift some of the gloom hovering over the travelling fans.
Most supporters who made the trip to Moscow will have been wondering why they bothered. Many only went out of loyalty and necessity in the end.
Had they known that such an inexperienced XI were to be sent into the cauldron of the Luzhniki staduim, most of the away support would have stayed at home.
But, to be fair, they can say that they were there when Bannan and Albrighton made their breakthroughs.
Young Scot Bannan showed he has good ability on the ball with some neat touches and a few forward runs and right winger Albrighton matched the excellent effort of his fellow academy graduate.
Anxiety
Both provided more danger to the Russians than they would have been expecting and Brazilian coach Zico looked rather uncomfortable throughout the first half.
Whether that anxiety was because of the Villa youngsters, who were teasing his full backs, or whether it was simply the sight of a fired up O'Neill patrolling the touchline no one can be sure.
Zico needn't have worried, though, as despite some neat passing and some good defending Villa never really threatened.
Protege Nathan Delfouneso looked isolated up front in the first half as he played a lone striking role and despite some surges from Craig Gardner and Steve Sidwell, he never really had the right service.
Gardner did have a goal ruled out near the end of the first half as he lashed the ball into the net in fine fashion only to see an offside flag raised.
Marlon Harewood was sent on at half time as Villa went with two up front but the away side struggled to create any real opportunities.
The best chance fell to Gardner, who controlled well on his chest and volleyed into the grateful arms of the Igor Akinfeev.
Validation
CSKA began to awake from their slumber and Brad Guzan had to be alert to save when one on one with dangerous winger Zhirkov.
But Villa couldn't hold out for long as the pressure grew and the home crowd grew more and more vociferous. It was Russian wideman Zhirkov who made the breakthrough as he cleverly worked a free kick with Alan Dzagoev before lashing the ball past Guzan with his left foot.
Villa tried to push their hosts in search of a goal which would have taken the tie into extra time but they couldn't find a way through and Vagner Love slotted in with seconds remaining to finish it off.
It was Love's goal in the first leg that proved vital and you get the feeling that had he not struck in the match at Villa Park the complexion of the tie would have been very different.
O'Neill may have felt his side had something to hold onto and consequently sent out a stronger side.
There is the possibility that he didn't really believe his full strength Villa side could progress and therefore he decided to prioritise.
Just as a school child chooses not to revise before an exam so as not to be disappointed, O'Neill sends out a weak side so he knew what he would get.
That may or may not be the real reason for leaving out eight first teamers but what is not in doubt is that Villa must now beat Stoke on Sunday.
O'Neill needs validation for his decision to forget the League Cup and Uefa Cup and finishing in the top four at the end of the season is the only way he is going to obtain it.