David Bellion's 19th-second strike was enough to beat Arsenal's youngsters and send Manchester United's second-string into the Carling Cup semi-finals.
A terrible blunder by Gunners keeper Manuel Almunia saw Bellion's weak shot squirm in after a Johan Djourou slip had gifted possession to Bellion.
The home side's greater experience was crucial and Kieran Richardson and Chris Eagles went close in the first half.
Arsenal's best chance saw Tim Howard beat out Jermaine Pennant's free-kick.
United, whose weakened line-up still included eight full internationals, got off to a dream start against an Arsenal side with an average age that dipped under 20.
A slip by Djourou allowed Bellion to run at the Arsenal defence.
And with defenders backing off and struggling to keep their footing, the Frenchman cut in from left to right before hitting a lame shot straight at Almunia which the Arsenal keeper somehow allowed to slip by him and into the net.
With Arsenal's youngsters still in shock, the home side had another great chance to double their advantage soon after.
Chris Eagles played a lovely one-two with Bellion and raced clear from left-back Gael Clichy but the teenager dragged his shot across the face of Almunia's goal.
John O'Shea also saw a looping header from a corner well dealt with by Almunia.
Tim Howard almost made a hash of a backpass on 26 minutes at the other end as he tried a smart turn with Van Persie bearing down on him.
But it was the home side, cheered on by a crowd of 67,103 crowd, who continued to look the more likely to score.
Almunia made an instinctive block from Richardson's full-blooded half-volley and the keeper had to rush off his line to clear from Bellion after an under-hit backpass from the otherwise impressive Philippe Senderos.
Howard made his first save of note in the 40th-minute, diving full length to push out Pennant's 20-yard free-kick.
Despite the frantic beginning to the first half it was not until the opening minutes of the second period that the match threatened to explode into life.
Scenes reminiscent of more famous United-Arsenal clashes of days gone by came to mind as Richardson and Van Persie clashed.
Both men could easily have been sent off for flailing arms but referee Mark Halsey opted to show yellow cards.
Arsenal were struggling to get enough possession to test Manchester United's experienced rearguard and the home side's greater strength was also telling.
The central midfield trio of Eric-Djemba Djemba, Liam Miller and Kleberson regularly outmuscled the Arsenal pair, Sebastian Larsson and Mathieu Flamini.
But despite the lively opening to the second period, the game was a non-event after that.
Eagles blazed wildly after neatly skipping past two Arsenal defenders but there was barely a chance to talk about as the home side comfortably held on to move into the semi-finals.
The only worrying sight came as United's Kleberson was stretchered off with an injury 11 minutes from time.
Man Utd: Howard, Phil Neville, Brown, O'Shea, Fortune, Eagles (Rossi 79), Djemba-Djemba, Miller, Richardson, Kleberson (Jones 79), Bellion.
Subs Not Used: Ricardo, Pique, Ebanks-Blake.
Goals: Bellion 1.
Arsenal: Almunia, Hoyte, Senderos, Djourou,
Clichy (Karbassiyoon 81), Pennant, Flamini, Larsson (Cregg 72), Owusu-Abeyie, Lupoli (Smith 68), Van Persie.
Subs Not Used: Simek, Wright.
Booked: Van Persie.
Ref: M Halsey (Lancashire).