An entertaining game in front of a lively, capacity 30,510 crowd, was a fitting way for Beckham to end his six seasons in MLS as he added another title to his collection.
"This is the goal we set ourselves at the start of the season," said Beckham. "It is another special occasion to win a championship at home, in front of our fans and our families."
L.A had to come from behind after Calen Carr put Houston ahead a minute before the break, breaking free down the Galaxy left and blasting in a near post shot, but the home side took control in the second half.
Defender Omar Gonzalez headed in the equaliser on the hour from a Juninho cross before Landon Donovan converted a penalty five minutes later to give the Galaxy the lead, after Ricardo Clark was ruled to have handled.
Striker Robbie Keane, who had two efforts disallowed, got his reward in injury time when Houston keeper Tally Hall tried to bring him down and the Irishman rose to slot home the penalty.
There was a moment of discussion between regular penalty taker Donovan and Beckham over who would take the kick, with many in the crowd expecting the Englishman to crown his farewell with a goal.
"I told Landon to take it but he said let Robbie take it because he was too tired," explained Beckham.
"I didn't want to take it, it's about winning the game, not about me taking the penalty to top things off," he added.
The former England captain received a standing ovation as he was substituted in the final seconds.
"I think today was always going to be an emotional day for myself, win or lose. I've been here for six years and part of a team that has kept the majority of their players together. Coming off was tough but I enjoyed the win today," he said.
After the final whistle, Beckham was joined on the field by his children as he said his farewell to the Galaxy fans after a display in which he had shown some of the passing vision and execution that has been characteristic of his career.
The midfielder has won league titles in his final season with all three of the clubs he has played with on a permanent basis - Manchester United, Real Madrid and now Galaxy.
"It never gets old, I'm 37 and I've been able to play in quite a few finals and championship games and I still love it like I did when I won my first," he added.
Galaxy's fourth MLS title equals the tally held by D.C United and the club said this week they intend to recruit another big name player to replace Beckham, having targeted Brazilian Kaka.
That may or may not be the next chapter in the Galaxy story but on Saturday one certainly closed as the most high profile soccer import in the United States since Pele in the 1970s, said goodbye.
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