Bolton may have lost at Villa Park after a first-half strike from Thomas Hitzlsperger and a late goal by Jlloyd Samuel but the foundation for their success had already been laid in the first leg at the Reebok Stadium last week that they won 5-2.
Villa had always faced a mountain to climb after that defeat but they did their best to overhaul the three-goal deficit - especially as they had to play for 51 minutes with ten men.
Their task was made all the more difficult after former England international midfielder Gavin McCann was sent off following a clash with the Bolton central defender Emerson Thome.
Hitzlsperger had given David O'Leary's side the perfect start with his tenth minute strike and Villa dominated the match and had opportunities to add to that advantage well before Samuel struck two minutes from time.
But a rugged Bolton side successfully rode their luck to secure their second appearance in the final - nine years after they were beaten 2-1 by Liverpool.
Villa should have been in front even before Hitzlsperger struck as Darius Vassell squandered a golden fourth minute chance when he shot straight at Jussi Jaaskelainen from just six yards out.
But Villa did not have to wait much longer for their high-tempo start to pay-off when Ivan Campo fouled Villa striker Peter Crouch on the edge of the Bolton area.
German Under-21 international Hitzlsperger left Jaaskelainen rooted to the spot when he curled home his 20-yard free-kick.
Villa should really have added to Hitzlsperger's strike before half-time but proceeded to waste their domination - and their frustration boiled over.
Samuel, Vassell and McCann were all booked for fouls within three minutes of each other. In an ill-tempered half, Bolton's Thome and Nicky Hunt also picked up bookings for a foul and time-wasting respectively.
After the flurry of yellow cards, Villa were again wasteful in front of goal when Crouch headed over the bar from six yards after being set-up by Lee Hendrie in the 35th minute before Gareth Barry missed the target as well from close range three minutes later.
Villa's task then become even more of an uphill battle when they lost McCann six minutes before half-time.
Having been booked only nine minutes earlier, McCann fouled Jaaskelainen. That could have earned him a second yellow card and a dismissal.
But the referee showed him a straight red card after he lashed out at Thome following the melee that followed his challenge on the Bolton keeper.
The loss of McCann was a blow that Villa struggled to overcome and they were unable to exert the same kind of pressure on Bolton as they had done before his dismissal.
While substitute Peter Whittingham did flash a shot wide at the start of the second half, Villa struggled to seriously test Jaaskelainen again.
Bolton, who were without their talisman, Jay-Jay Okocha, who was on African Nations Cup duty with Nigeria, enjoyed far more of the play in the second period and could have eased their nerves - and ended Villa's challenge - if Youri Djorkaeff had been able to direct his 62nd minute header on target.
Kevin Davies also wasted a good opening when he outpaced the Villa skipper Olof Mellberg after 77 minutes only to drag his angled shot wide from 16 yards when he was faced with only goalkeeper Thomas Sorensen to beat.
Villa then set up a thrilling finale when Samuel fired into the roof off the net after a run by Crouch but it was too little too late for Villa.