Liverpool went in front after four minutes when John Arne Riise scored from 25 yards and Michael Owen doubled their lead from the edge of the area.
Cisse hit the post before scoring after a one-two with Danny Murphy then Stephane Henchoz notched with a shot that looped over keeper David Marshall.
Craig Beattie scored from the penalty spot for Celtic before Cisse's second.
Celtic assistant manager John Robertson and coach Steve Walford made 10 changes from the team that lost to Chelsea in their opening game of the Champions World Series.
Scott Cuthbert, 17, made his first start and 18-year-old Aiden McGeady played in midfield.
But Liverpool, with Milan Baros playing alongside Owen, dominated from the start.
Celtic keeper Marshall, just 19, fumbled an Owen cross and it bounced off Ulrik Laursen's feet to Harry Kewell, but his shot was blocked.
Dietmar Hamann laid off a free-kick for Riise to open the scoring, but Celtic almost equalised when Chris Kirkland fumbled McGeady's cross.
Owen's goal, on 17 minutes, came after Riise lobbed the ball over a flat-footed Joos Valgaeren.
Vladimir Smicer missed a great chance to score a third after Baros played him through, while at the other end John Hartson headed a McGeady corner wide of Kirkland's goal.
Liverpool coach Rafael Benitez made six changes at half-time, including the introduction of Cisse and Steven Gerrard.
Celtic made four changes but the momentum remained with Liverpool.
Cisse hit the post after being played through by Florent Sinama-Pongelle, while Neil Lennon could have been dismissed for a lunge on Kewell.
Cisse opened his account for Liverpool on 62 minutes before Henchoz's freakish goal, with the ball bouncing off the turf and looping over Marshall.
France striker Cisse should have made it five moments later when he was put clean through but he chipped the ball straight into the hands of Celtic's young goalkeeper.
Beattie, after his double at the weekend, gave the Glasgow side a consolation in the 72nd minute from the spot after Salif Diao had brought down the youngster.
But Cisse notched his second of the night in the 76th minute when he received Murphy's pass and cut inside Slatislav Varga before firing low under Marshall.
Benitez, though, felt Cisse might have scored more.
"He got two goals but he could have perhaps had two more," Benitez said of Cisse. "But there were a lot of positives and there were other people on the scoresheet.
"We now have four top strikers who are different players and for me the four forwards did well. I can't decided between them at the moment."