Controversial second goal taints stylish win.
The visitors took the lead just prior to the break in comical circumstances as a headed effort was sliced off the line only to smack the back of keeper Tim Krul's head and bounce into goal.
Theo Walcott added a second after dinking the ball over Krul, but Nicklas Bendtner's involvement in the goal had St James' Park fuming as, from an offside position, he deliberately blocked the path of Mike Williamson who was racing down on goal to block the England man.
The Danish striker notched one himself with a stellar finish with time running out after bending a shot beyond Krul before Walcott wrapped things up with minutes remaining.
Both managers made nine changes to their sides that played in the Premier League at the weekend, with the notable youngsters on show for the home side being Tamas Kadar, Haris Vuckic and Nile Ranger, who netted in the stunning away victory in the previous round at Chelsea.
Meanwhile Arsene Wenger named a strong line-up after abandoning his policy of playing solely youth players in the competition, with only Craig Eastmond and Polish stopper Wojciech Szczesny being considered rookies in an otherwise strong XI with Cesc Fabregas starting from the bench.
The somewhat experimental make-up of both teams made for an entertaining opening as each side sought to test the other, with Carlos Vela being denied by a bold save from Tim Krul, who was on hand moments later to bat away a Bendtner effort.
The men in black and white soon showed their attacking intent as they surged towards goal before Vuckic launched a strike from distance that rippled the outside of the net.
Minutes later and the visitors were launching more attacks of their own, but Theo Walcott spurned a chance to gift Vela a tap-in by misplacing a cross to the Mexican forward after Emmanuel Eboue had seen a low drive well saved by Krul and Bendtner saw an a strike drag wide.
The excitement didn't stop there though as the Magpies created the first clear cut chance of the game when Ranger's burst of pace enabled him to slip beyond the Arsenal back-line and latch onto a Danny Guthrie punt, but the young striker, after beating Szczesny, dallied before seeing a timid effort blocked away by Laurent Koscielny.
From the resulting set-piece the ball fell to former Manchester United midfielder Alan Smith, who hit a stinging drive that smashed off the bar after the Polish keeper managed to divert it via the slightest of touches.
Wenger was soon called into making an unanticipated change as Kieran Gibbs, who had picked up a knock in the opening minutes that necessitated treatment, struggled to get back up to speed and had to be replaced by Bacary Sagna.
That change enabled both sides to take a breather after 20 minutes of relentless action, and following the swap the pace dropped significantly, although Newcastle did appeal for what would have been a highly fortuitous penalty after the ball hit substitute Sagna in the box.
What had started as a high octane and open game soon turned cagey with neither team carving out clear opportunities, and Bendtner wasted a scarce chance after tamely rolling the ball to Krul following a confident run into the box.
Similarly, Emmanuel Eboue strode into the area from a left-sided position after beating Ryan Taylor with a drop of the shoulder, but the Ivorian futilely elected to shoot from a tight angle with Vela in space.
The Gunners were, however, exerting their control of the game with much of it being played in Newcastle's half and arguably should have had a penalty after James Perch misread a cross and first scraped Johan Djourou before then seeming to handle the ball.
Arsenal finally capped off a dominant spell by opening the scoring, but it was hardly a goal befitting their sophisticated play. A Vela corner was headed towards goal by Bendtner and, after bouncing off several bodies, the ball was nodded off the line by Taylor and rebounded into the net off the back of the unfortunate Krul's head.
That comical goal was the final act of a first half that had plenty of action, and plenty of missed chances, but the lead was a deserved one for an Arsenal side that had comfortably controlled the final 20 minutes of action and should have already opened the scoring, with Bendtner in particular guilty of wasting several decent opportunities.
Krul to be kind | Gaffe gifts Arsenal lead
Neither Chris Hughton nor Wenger opted to make a change for the restart, from which Newcastle captain Smith saw himself go in the book after a sliding tackle on Walcott tripped the zippy forward as he attempted to deliver a cross.
The home side soon had an opportunity to level the score from a corner, but after leaping like a salmon, Perch looked like a fish out of water as his header flew over Szczesny's bar.
The visitors then extended their lead in controversial fashion. Danish striker Bendtner, returning from an offside position, jogged into and collided with Williamson, allowing Walcott to race through unopposed and lift the ball over Krul as referee Andre Marriner refused to blow for an infringement.
Hughton swiftly thrust on winger Jonas Gutierrez and striker Andrew Carroll, for the ineffective duo of Wayne Routledge and Peter Lovenkrands respectively, but neither substitute was able to make an immediate impact as the Gunners continued in much the same fashion as they ended the second half, retaining possession with relative ease.
Gutierrez did, however, offer the home fans something to cheer about with some direct running at Sagna, who conceded a corner after blocking a shot from the Argentinian, and fellow substitute Carroll should have utilised his aerial might but could only nod wide at the far post from the set play.
Wenger was afforded the chance to give Cesc Fabregas a rare run out in the early stages of the Carling Cup as he replaced the tiring Vela, who had been the quietest of Arsenal's front trio, while Hughton also threw his last roll of the dice by making a like-for-like change as Smith was hooked off for Joey Barton.
Newcastle continued to prod away, and saw an effort scrambled off the line, but it came as no real surprise when Arsenal wrapped up victory with a third after Bendtner finished a sweeping team move with a superb strike on the edge of the area.
The Danish striker was quickly hauled off for Jay Emmanuel-Thomas, but Arsenal didn't stop scoring there as Walcott raced clear after being released by Koscielny and coolly slotted past Krul.
Carroll came close to netting a consolation goal with the final chance of the game only to be denied by Szczesny, and the margin of victory did not flatter the visitors who had strolled in the second half.
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