After the game had ended 1-1 after 90 minutes, the former Fulham keeper kept out efforts by Claudio Pizarro, Frank Lampard and Shaun Wright-Phillips as last term's Premier League champions won 3-0 in the shoot-out.
Rio Ferdinand, Michael Carrick and Wayne Rooney all slotted home their penalties as United clinched victory in a tight game they just about edged.
Jose Mourinho's side badly missed the injured Didier Drogba and John Terry and, despite having lots of possession, suffered from a lack of a cutting edge.
A quiet opening revived memories of the dreadful FA Cup Final between the two teams less than three months ago, but the match livened up midway through the first half.
In the 22nd minute Cristiano Ronaldo set up Ryan Giggs whose right-foot shot was blocked by Petr Cech when the veteran Welshman should really have broken the deadlock.
Almost immediately Michael Carrick dragged a shot from just outside the area narrowly wide while at the other end Michael Essien's header was inches off target as John Obi Mikel just failed to supply the finishing touch.
Ten minutes before the break, the outstanding Patrice Evra got to the byline after good play by Nemanja Vidic and Ronaldo, and pulled the ball back for Giggs to lift a shot into the roof of the net.
Chelsea appeared to have run out of ideas but they shocked United by equalising just before the break. Ashley Cole played in Florent Malouda and the powerful Frenchman held Ferdinand off before flicking a left-foot shot past Van der Sar.
The second half started quietly on a hot and sticky Wembley afternoon until Cech was forced to block a Ronaldo effort.
Pizarro dragged a shot wide while Vidic was unfortunate not to win a penalty when appearing to be pushed in the back by Tal Ben Haim as the two players tried to get their head to a cross.
A flurry of late substitutions stopped the flow of the game and gave Van der Sar the chance to be the first shoot-out hero of the 2007-08 season.