Beckham scored his penalty but Galaxy captain Landon Donovan was among those to miss as Salt Lake won the shootout 5-4 to capture a surprise victory just four years after entering the league.
Galaxy took the lead four minutes before the break through Mike Magee, who turned in a low cross from Donovan after good work from Beckham, but Salt Lake equalised in the 64th minute when Robbie Findley blasted in from close range.
After a scoreless extra-time, the shootout went into sudden-death and the Galaxy's Edson Buddle had his shot saved by Salt Lake keeper Nick Rimando before Robbie Russell slotted home to secure the championship.
"Its always tough losing, whether it be penalties or normal play but of course we can be proud of where we have come to," said Beckham, whose team reached the championship final a year after having one of the worst records in the league.
DESERVED WINNERS
Salt Lake were crowned champions, in front of a 46,000 crowd at Seattle Sounders' Qwest Field, despite having lost more games than they won in the regular season.
But Beckham, who had three injections in his right ankle before the game, said that Salt Lake deserved their success.
"They deserved to be here and they deserved to win tonight in the end," the midfielder told reporters.
The scrappy game featured a number of injuries and ended with both teams looking exhausted as a limping Beckham, who played with bruised ankle, struggled through the extra-time period.
Galaxy coach Bruce Arena said that Beckham was one of several players on his team who were not fully fit for the game.
"There are probably very few players that are 100 percent, this time of the year. No, he was obviously a little bit hobbled, certainly wasn't 100 percent," he said.
The England midfielder was involved an early incident when his challenge on Salt Lake's Argentine playmaker Javier Morales left the player needing to be substituted.
Rimando continued his fine record in shootouts, adding to his three penalty blocks in the Conference final win over the Chicago Fire with a further two saves on Sunday.
Real coach Jason Kreis felt justice had been done.
"We deserved to win the game... we are the best team in this league," he told reporters.
Arena agreed that the result was a fair one, saying: "We didn't play well enough over the 120 minutes to win the game."
