Cristiano Ronaldo's strike on the quarter-hour mark was cancelled out by Frank Lampard's goal just before the break.
After an extra time, during which United and Chelsea failed to score, the game went into penalties.
Ronaldo could have been the culprit when he wasted United's third spot kick following two successful attempts from Carlos Tevez and Michael Carrick.
However, John Terry's fifth penalty, which would have handed Chelsea a priceless win, struck the outside of the post.
After Giggs converted United's seventh spot kick, French striker Anelka's effort was blocked by Dutch guardian Van der Saar.
United ensured it would be a night to remember after securing their third Champions League title in history.
They also completed the double as they won the Premiership after a stiff competition from Chelsea.
United's Dominance
United were by far the better side in the early stages of the game.
Scottish coach Alex Ferguson switched Ronaldo to the left flank to avoid a usual tough contest against Ashley Cole.
Ferguson's decision was effective as Ronaldo repeatedly overcame challenges from Ghanaian midfielder Michael Essien, who played as a right-back.
Ronaldo and Owen Hargreaves provided several dangerous crosses but Wayne Rooney and Carlos Tevez couldn't capitalize.
The Portuguese broke Chelsea's resistance in the 16th minute when he towered above the motionless Essien to head home Wes Brown's left-footed cross from the right flank.
A moment of brilliance from Chelsea's keeper Petr Cech denied United's second goal of the night.
In the 35th minute, Cech denied Tevez's close-range header before blocking a fierce drive from Michael Carrick on the rebound.
Lampard was lucky to draw Chelsea level just before halftime through an opportunist strike.
Essien's shot from the edge of the area took a deflection before bouncing off Rio Ferdinand's back.
Consequently, Van der Saar was wrong-footed, to allow Lampard slot into an empty net.
Chelsea's Improvement
Chelsea notably improved in the second period and managed to dominate possession for large periods.
Essien succeeded in stopping Ronaldo's threat in the second half after struggling against the former Sporting Lisbon ace during the first period.
Nemanja Vidic and Ferdinand were also successful in their marking of Didier Drogba.
However, the Ivorian hitman came close to putting his side ahead in the 78th minute but his superb curling shot was denied by the post.
United's Welsh winger Giggs made a record 759th appearance for the Red Devils when he replaced Paul Scholes with four minutes remaining.
Neither side managed to score as the match went into extra time.
Chelsea had a glorious opportunity to break United hearts four minutes into the first-half of extra time.
Michael Ballack muscled his way into United's area before feeding Lampard. The England defender turned and shot goalwards but his effort struck the crossbar.
At the other end, Chelsea had to thank inspirational captain Terry for denying United the lead.
Patrice Evra beat three challengers and evaded a Cech challenge to pull back to Giggs', whose shot was blocked by Terry's header.
Chelsea finished with ten men after Drogba was sent off for slapping Vidic shortly before the end.