With Jeremie Aliadiere and Alexandre Song also on target, the young Gunners completed a cup double over Rafael Benitez's side in the space of three days. They triumphed at the ground in the FA Cup at the weekend and although Robbie Fowler, Steve Gerrard and Sami Hyypia all scored, the Kop were again left in a state of disbelief. England manager Steve McClaren and his right hand man Terry Venables both attended the match, possibly to monitor Theo Walcott's progress at Arsenal.
Liverpool boss Benitez had to make a change after only five minutes when Mark Gonzalez's leg buckled under him as he tried to make a challenge.
The Chilean was in some distress and given oxygen on the pitch before being carried off on a stretcher.
The on-field treatment lasted five minutes and he was replaced by Luis Garcia.
Liverpool came close to making the breakthrough in the 14th minute when Gerrard got on the end of a cross from Craig Bellamy.
The England midfielder powered in a header that was cleared by Justin Hoyte.
Garcia then set up Stephen Warnock and he delivered a good ball into the area that was anticipated by Almunia.
Almunia was tested again in the 18th minute when Gerrard rattled in a shot from distance.
The Arsenal goalkeeper responded by getting down quickly to make a comfortable save.
The visitors were again on the back foot in the 22nd minute when Bellamy tried to pick out Robbie Fowler but over-hit his cross.
Arsenal made the breakthrough in the 27th minute following a long ball from Toure.
Jeremie Aliadiere reacted quickly and skipped between Lee Peltier and Gabriel Paletta to fire a shot at Dudek who parried and the forward netted the loose ball.
Liverpool hit back five minutes later after Fowler was tripped by Alexandre Song as he raced forward.
Fabio Aurelio's free-kick 25 yards out was pushed away by Almunia but only as far as Garcia.
The Spaniard neatly played the ball in to Fowler and he applied a clever finish from close range for the equaliser.
It was Fowler's fifth goal in 13 matches - and game on in front of an expectant home crowd.
Gerrard then worked an opening for himself in the 39th minute only for his effort from an acute angle to be deflected to safety.
Arsenal regained the lead in the 41st minute with a stunning free-kick from Julio Baptista.
He lofted the ball over the wall and beyond Dudek, who was left rooted to the spot.
Song made it 3-1 to Arsenal in stoppage time although he seemed to know little about it, the ball coming off his body after Fabregas had swung in the corner.
It was becoming a rout with Baptista scoring his second goal of the game following a neat one-two with Aliadiere.
HT: Liverpool 1 Arsenal 4
Liverpool were desperate to begin the second half with a bang and Garcia tried to pick out Bellamy in the 52nd minute but Almunia was alert to the danger and made the clearance.
Baptista should have claimed his hat-trick and made it 5-1 to Arsenal in the 58th minute.
But he saw his penalty brilliantly clawed away by Dudek, much to Liverpool's relief.
The spot-kick was awarded after Hyypia had tussled with Aliadiere and the central defender was furious at the decision. He seemed to have a case.
However, Baptista shrugged off his misery and was celebrating on the hour.
He rattled in a shot from the edge of the area after Gerrard had failed to cut out a cross from Aliadiere.
Baptista was on the top of his game, his strength and movement causing problems for Liverpool.
The Kop could hardly believe what was unfolding before their eyes and the young Gunners continued to play with menace every time they pushed forward.
However, Gerrard pulled a goal back in the 68th minute with a magnificent volley and suddenly Liverpool began to look threatening.
Gerrard almost got a third goal in the 80th minute but Almunia managed to push his effort on to the bar.
A minute later Hyypia gave Liverpool a glimmer of hope by heading home following a cross from Gabriel Paletta to reduce the deficit to two goals.
Baptista, on loan from Real Madrid, was on a roll and got his fourth of the night in the 83rd minute after again being set up by Aliadiere following a swift counter-attack.