The Galaxy controlled the game from the beginning and eventually found the back of the net late in the second half thanks to their three star players
The Galaxy capped off a fantastic regular season that saw the team pick up a league-leading 67 points by winning their third title in front of a packed house on their home ground.
Donovan was awarded the MLS Cup final MVP after scoring in the 72nd minute on a play that was set up by both Beckham and Keane.
It was a fitting ending to what could have been Donovan's final game playing alongside Beckham, whose historic five-year deal with the Galaxy is now over. And Donovan had nothing but praise for his longtime team-mate while accepting his MVP award.
"He pulled his hamstring earlier in the week and was basically playing on one leg tonight," Donovan said. "He put in a warrior-like effort and I'm real honoured to play next to him."
Beckham now has won titles in three different nations - England, Spain and now the United States. He was, however, unclear about a potential return to the MLS after the game.
The Galaxy were in the driver's seat early on and Beckham nearly set up the first goal of the game off a corner kick in the 11th minute, but Adam Cristman's header from point-blank range sailed over the crossbar despite being unmarked right in front of the goal.
Nearly 16 minutes later, the Galaxy duo was at it again. This time, Beckham placed a cross to Cristman, who snuck past the defence but watched his header rise above the bar.
The Galaxy continued to put the pressure on the Dynamo in the closing stages of the first half, leaving Houston with no real scoring opportunities in the first 45 minutes. And Los Angeles would pick up right where it left off after half-time.
Just three minutes after the break, Keane beat the offside trap to latch onto a deflected long pass and found himself one-on-one with goalkeeper Tally Hall. Slightly off balance, the Irish international skipped the ball just inches wide of the far post in yet another golden opportunity for the hosts.
Moments later, it appeared as though Keane had finally broken the deadlock when he put a strike through Hall's legs into the net. But as the fans were celebrating, the referee held up the offside flag on a controversial offside call. Replays, however, suggested that he was indeed level with the defender when Beckham delivered the ball.
But the Galaxy would eventually get their goal in the 72nd minute thanks to their three most expensive players. Coming down the left side of the pitch, Beckham tapped the ball to Keane, who then touched it to Donovan to apply the finish with a right-footed shot.
Beckham nearly completed the ideal ending to what could have been his final MLS game when his free kick from just outside the box was saved by Hall in the closing seconds.
The Dynamo did not have a chance from the beginning as they were without league MVP finalist Brad Davis, who went down in the Eastern Conference final with a torn quad. Davis was replaced in the midfield by left back Corey Ashe and Jermaine Taylor filled in at the defensive spot, but neither player could fill his shoes.
For the Galaxy, the win marked Galaxy head coach Bruce Arena's record-setting third triumph in the league's championship after leading his squad to a perfect record at home during the regular season and play-offs, including a 1-0 victory over Houston back in May.