Ninety three incident-filled minutes ended with the FA Cup winners and Premier League champions level at 2-2.
The Blues lifted the shield following a comprehensive victory in the shootout, with Ryan Giggs and Patrice Evra missing their spot-kicks.
Textbook 12-yard efforts from Frank Lampard, Michael Ballack, Didier Drogba and Salomon Kalou sealed a first trophy win at Stamford Bridge for new manager Carlo Ancelotti.
The two sides were even throughout regular time, but a stoppage-time Wayne Rooney equaliser cancelled out a controversial Lampard goal to make it 2-2.
It was Sir Alex Ferguson's side which started the game the brighter, having the better of the first half, despite the first chance of the game falling to Branislav Ivanovic of Chelsea.
From a corner, the full-back crashed a volley into the ground which was headed onto the crossbar by Evra, providing a narrow escape for the champions after just six minutes.
But the rest of the half belonged to United, with the first goal of the game coming four minutes later.
Nani, who was the star of the show in the first period, danced his way inside from the left wing to fire a bouncing shot from 25 yards, which evaded Petr Cech at his far post.
The rest of the first half saw United dominate, with Rooney and Dimitar Berbatov linking up well.
Nani also showed his worth to Sir Alex Ferguson in his bid to succeed fellow countrymen Cristiano Ronaldo as United's wing hero, but the Portuguese player was forced off in the second period favouring his arm, in what could be a serious injury.
Chelsea appeared for the second half with a new sense of purpose and were rewarded with an equaliser on 52 minutes.
Ricardo Carvalho crept into the United area unmarked and casually nodded the ball into an empty net after Ben Foster parried a meaningless cross.
And their comeback was complete when Lampard netted 20 minutes later.
The goal did not come without controversy, as referee Chris Foy allowed United an advantage with Evra on the floor holding his face after being body-checked by Ballack. Moments earlier, Foy brought play to a halt when Ballack was on the ground.
But this time play continued, with Chelsea winning the ball back and racing forward. Lampard completed a simple attack, netting after the Red Devils were outnumbered in defence. This was to the fury of United's players, particularly Rooney.
The match became disjointed in the last half hour, but substitute Giggs came up with a final piece of magic in the second minute of injury time.
A delightful pass behind the Chelsea back four saw Rooney race onto the ball, before neatly chipping over to earn a draw.
But it all proved academic in the end result, as the brilliant penalty-taking technique of Chelsea secured an easy shootout win.