Omar Gonzalez and Donovan scored within minutes of each other to overcome Calen Carr's 44th-minute opener for the Dynamos, and the Galaxy added a stoppage-time penalty from Keane to capture their second consecutive MLS Cup title and send Beckham out of MLS as a two-time champion with a 3-1 victory in front of a sellout crowd of 30,510 at the Home Depot Center.
The Galaxy had their fair share of chances to get on the board earlier in the game but couldn't convert. Donovan missed the most golden of the chances in the 13th minute. Beckham picked out Keane down the left with a trademark long pass out of the back, and Keane set up the American perfectly from point-blank range. The Galaxy captain's first-time effort went wide of the mark though, as confetti cannons at the Home Depot Center shot off in anticipation of the finish.
The Galaxy then had another great chance in the 20th minute, with Beckham serving a pinpoint free kick from the right to the far post, where Mike Magee's close-range header went over the bar. Keane then had an apparent-equalising goal waved off in the 48th minute after a redirected Beckham free kick was sent in Keane's path, but the Irishman was in an offside position as he fired past Hall.
Houston goalkeeper Tally Hall had punched away a Beckham corner kick, but the ball worked its way back to Sean Franklin and then to Juninho, who's perfect ball from the right to Gonzalez was headed home in the 61st minute.
The Dynamo had taken the lead through Carr just before half-time. Adam Moffat played the speedy forward down the right, where he beat Tommy Meyer for pace and was kept onside by Gonzalez. Carr took a touch toward goal and finished with a drive past Josh Saunders as Meyer tracked back to recover, giving Houston a huge momentum swing heading into halftime.
Carr had been out with a left hamstring strain, missing the Eastern Conference final series against D.C. United but regained fitness at a perfect time for the Dynamo. He had a would-be second goal robbed by Saunders, who dived to his left to snatch a point-blank header from Carr off a cross from Will Bruin in the 56th minute. He departed soon after with an apparent leg injury after colliding with Gonzalez, though, and the Galaxy promptly equalised moments later.
Donovan netted the second (his MLS record 22nd postseason goal and record fifth MLS Cup goal) from the penalty spot in the 65th minute, after a scramble in the area resulted in a handball by Ricardo Clark. That came moments after Gonzalez headed home the equalizer off a cross from Juninho.
Keane got his in the dying seconds, though, earning a penalty on Hall off a breakaway and firing home from the penalty spot to seal the victory.
With the victory, Donovan has a record-tying five MLS Cup triumphs, Bruce Arena has an MLS-record four as a coach and the Galaxy tied D.C. United with a league-best four MLS Cup titles.