Chelsea, who won the domestic double last season, could not match a United side inspired by evergreen midfielder Paul Scholes, who produced a superb passing display.
United and Chelsea's England players were booed by fans at Wembley Stadium every time they touched the ball in the early stages of the game following the team's dismal showing at the World Cup.
Winger Antonio Valencia put United ahead four minutes after the break when he was found unmarked by a low cross from Wayne Rooney to fire home from close range.
Javier Hernandez scored his first goal for United in the 76th minute to double their advantage.
In a fortuitous fashion, the ball bounced off the Mexico striker's face and into the net after a Valencia cross.
Salomon Kalou pulled one back for Chelsea six minutes from time after United keeper Edwin van der Saar parried a shot from Daniel Sturridge into his path.
However, substitute Dimitar Berbatov ensured United's win in stoppage time with a superb lob.