The charismatic star completed his miraculous comeback from a broken leg in October to all but guarantee himself a place in the starting line-up against AC Milan in ten days.
Cisse made his first start since breaking his leg in October and there were chances for fringe players Stephen Warnock, Igor Biscan and Harry Kewell to press their claims for a final berth.
For the visitors, boss David O'Leary handed Nobby Solano and Eric Djemba-Djemba returns to the starting eleven after coming on from the bench in last week's home defeat by Manchester City.
There was no place in the squad for the departing Thomas Hitzelsperger, who is returning to Germany with Stuttgart in the close season.
Lee Hendrie, stung new England call-up Scott Carson's fingers with a curling drive after just two minutes, which proved to be the only goalmouth action in an uneventful, somewhat lethargic opening.
It took an unlikely source to kick Liverpool into life as centre-half and captain for the day Jamie Carragher surged forward through the entire Villa side and drove a shot into the sidenetting.
A minute later the Reds had a penalty and the lead through the enigmatic Cisse. Kewell's blistering shot was parried into the path of the Frenchman, who was recklessly hacked down by Mark Delaney.
Cisse picked himself to drive an unstoppable spot-kick into the bottom corner, his first goal since making a miraculous recovery from a career-threatening leg break.
Cisse, almost certainly sealed his place in the starting line-up in Turkey with a second on 27 minutes, tucking away with his right foot after a mazy run and cross by fellow long-term injury victim Josemi.
Former AC Milan centre-half Martin Laursen may be on the phone to Paolo Maldini and co to heed a well-justified warning ahead of the final. Cisse is back.
Cisse began the second period in much the same vein, brilliantly bringing the ball down to feed Antonio Nunez, whose shot was well stopped by Thomas Sorensen.
But Villa, who made two changes after the break, weren't dead and buried and an error from Mauricio Pellegrino allowed substitute Luke Moore a sight of goal, but Carson blocked well.
An indeed they pulled one back with 23 minutes left on the clock, as a mix-up in the home defence allowed skipper Gareth Barry to fire in unmarked from six yards.
Villa continued to press after more and more mistakes in defence, mistakes more likely to be punished by Andriy Shevchenko in Turkey.
But Liverpool regained their composure late on with fine long-distance efforts from Cisse and John Arne Riise, who hit the bar, as they sealed a morale-boosting triumph and fifth place in the table.