Chelsea Captain John Terry glanced home a 76th-minute free-kick from Frank Lampard to snatch a 1-0 win, although United claimed Didier Drogba was in an offside position.
Manchester United had their chances with Wayne Rooney twice going close but the Blues made it a club record of 11 straight home wins.
It was the home side who created the first goal attempt when Branislav Ivanovic burst down the right flank and let fly with a left-foot shot which Edwin van der Sar did well to hold at the near post.
Manchester United though were far more comfortable on the ball with the home side given little time to build from the back.
But a long cross from Michael Ballack in the 18th minute found the lurking Drogba on the edge of the six-yard box but the Didier Drogba failed to direct his header on to the target.
Manchester United, despite their dominance, had not created a clear cut chance.
In the 23rd minute, Chelsea won a free-kick but Lampard wasted the chance to test the United defence when he sent his curling effort beyond the far post.
Drogba was fouled by Wes Brown in the 27th minute in a central position 25 yards from goal.
It was another chance for the home side but again Lampard's free-kick was poor as he sent his effort straight into United's defensive wall.
Moments later Nicolas Anelka tried to beat Van der Sar from 35 yards but the United keeper dealt with it most comfortably.
Van der Sar was tested again when he made a one-handed save to keep out a curling shot from Anelka in the 32nd minute.
A quick counter attack from Chelsea saw Anelka put Deco free on the right flank but his cross eluded Ballack before arriving at the feet of Drogba. The Ivory Coast striker was unable to control the ball and it ran harmlessly into the arms of Van der Sar.
Drogba then broke into the penalty from the right flank but his angled drive ended in the upper tier of the stand as referee Martin Atkinson brought proceedings to a finish for the opening period.
In the 50th minute Drogba got the better of United's John O'Shea but his 25-yard shot went wide of the target.
Ivanovic was booked for a foul on Giggs in the 57th minute as the game began to open-up.
Ricardo Carvalho managed to get his body in the way of a fierce shot from Darren Fletcher moments later. It was a fine piece of defending by the Chelsea man.
A cross from Anelka fell kindly to Lampard on the edge of the penalty area but the England midfielder's shot was easily saved by Van der Sar.
Chelsea had gone over 14 hours since they last conceded a goal at Stamford Bridge.
It was time for the home side to make a change and Carlo Ancelotti opted to remove Deco in favour of Joe Cole, who was celebrating his 28th birthday.
Rooney should have punished Chelsea in the 66th minute when he took a return pass from Antonio Valencia on the edge of the penalty area. But the England striker sent his shot a foot wide of the far post.
Seconds later Rooney brought a fine save from Petr Cech with a 20-yard curler which was destined for the top corner until the Czech international intervened.
There was a worrying moment for Chelsea in the 71st minute when Drogba was kicked in the chest by Jonny Evans. Astonishingly, Drogba was then booked by Atkinson.
Chelsea were in front in the 76th minute when Ashley Cole was fouled by Fletcher on the left flank. Captain Terry rose to glance Lampard's free-kick into the corner of the net but United were furious that Drogba appeared to be in an offside position as the ball bounced beyond Van der Sar and into the net.
Wayney Rooney was booked afterwards and then Atkinson booked O'Shea and Carvalho in the 82nd minute as tempers flared. Valencia was lucky remain on the pitch with a two-footed challenge on Lampard but Atkinson handed him a yellow card.