But United withstood the blitz and came roaring back themselves to take the points and go six clear of second-placed Chelsea, who entertain Wigan on Monday.
United now go to Chelsea in just under a fortnight sure of being ahead of the Londoners when the teams meet.
The game was a classic with the usual animosity between the sides so often apparent giving way to some brilliant football as both these titans of the English game battled to the end.
Arsenal dominated the early exchanges but United were twice let off the hook by Emmanuel Adebayor's profligate finishing. United had their chances with Wayne Rooney also going close twice.
But if the first half was mouthwatering, the second was a feast of magnificent football.
The stage was set when the Gunners took the lead three minutes after the interval.
Alex Hleb found Cesc Fabregas who rolled the ball on to Robin van Persie on the left side of the United box. The Dutchman's cross into the centre was missed by Rio Ferdinand and, with United goal keeper Edwin Van der Sar and Michael Carrick leaving the clearance to each other, Adebayor nipped in to head home his 26th goal of the season.
Back stormed United and when Carrick's innocuous ball into the Arsenal box was handled by captain William Gallas, referee Howard Webb pointed to the penalty spot.
Up stepped Cristiano Ronaldo to drive the ball right-footed into the top right corner of the net, but Mr Webb ordered the kick to be retaken when it appeared that United's Ji-Sung Park had encroached into the box.
The Portuguese star kept his nerve with the second kick again right-footed only this time low and into the bottom corner of the net beyond Jens Lehmann's despairing dive. It was Ronaldo's 38th goal of the campaign.
Van der Sar saved well from Ferdinand's attempted clearance of an Adebayor cross, while at the other end Lehmann's fine save with his legs denied Rooney.
Gael Clichy's cross from the left was deflected onto the United post by Wes Brown but in the 72nd minute Old Trafford went wild.
Gallas brought down Patrice Evra two yards outside the Arsenal penalty area in a central position. Ronaldo shaped up to take the kick but Owen Hargreaves stepped in to curl a glorious right-foot free-kick just inside the right post with Lehmann standing glued to the spot.
In the closing stages Van der Sar produced two tremendous saves to keep out headers from Nicklas Bendtner, but time finally ran out for Arsenal's dreams.