Second-half goals from Sanchez Watt and Carlos Vela were enough to confirm progression as the Gunners completely dominated the latter stages of the encounter.
Apart from a brief spell midway through the first half, Roberto Di Matteo's charges were given a footballing lesson by Arsene Wenger's boys.
Philippe Senderos had two great chances to put the Gunners in the lead in the opening five minutes when he lost his markers to meet accurately delivered Jack Wilshere corners but both efforts flew agonisingly wide.
Sanchez hit the base of the post with Dean Kiely beaten on the 17th minute and immediately, at the other end, Simon Cox and Robert Koren forced rookie keeper Wojciech Szczesny into two fine saves in quick succession.
Jack Wilshere fired a 25-yard drive just wide of Kiely's goal on the half-hour as the young Gunners grew in confidence.
The game got heated when former Gunner Jerome Thomas gave referee Lee Mason no option but to dish out a red card after he smacked Wilshere following a confrontation as the two tangled.
Thomas' discipline, one of the reasons he was released by the Gunners, had made the task his team-mates faced considerably tougher.
Di Matteo shuffled his pack slightly and the visitors held on, but Arsenal took the lead in the 68th minute when Aaron Ramsey slipped in Vela, whose fierce shot was only half saved by Kiely.
Watt was alert and on hand to fire home the rebound from close range. It was a just reward for the hard-working youngster and the goal seemed to further inspire the young Gunners.
Vela put Arsenal 2-0 up on 76 minutes after a smart Mark Randall chip left Kiely rooted to the spot but relieved to see the effort bounce back off his bar.
But the Gunners' Mexican striker reacted quicker than Kiely and Leon Barnett to latch on to the ball and then fire into the roof of the net from a yard out.
Chris Wood spurned a golden opportunity at the end of the match to reduce the arrears but his volley flew well wide with just the keeper to beat.
But even if he had converted, it would have been too little too late as the referee blew up for full-time shortly after.