Jerzy Dudek replaced Chris Kurkland in goal, Anthony Le Tallec was given a place alongside Emile Heskey in attack, Jon Otsemobor was handed a place at right back and Vladimir Smicer,John Arne Riise and Danny Murphy returned to the side, with Murphy wearing the captain's armband.
Mario Jardel scored for the visitors after only four minutes. Danny Murphy headed the Reds level on 66 minutes, but it wasn't long before the Trotters were ahead again - Jay Jay Okocha curling a free kick past Dudek.
The home fans thought Liverpool had saved the game when Smicer hit the back of the net from 30 yards out with two minutes remaining, but Salif Diao brought down Kevin Davies in thje area in the dying seconds to allow Djorkaeff to score from the penalty spot.