Trailing 1-0 at the half in the MLS Cup, the Galaxy began their comeback in the 60th minute when Omar Gonzalez scored the equalizer on a header following a corner kick and an assist by Juninho.
Four minutes later, Houston's Ricardo Clark was cited for a hand ball in the penalty area and Donovan converted the resulting penalty kick to put the Galaxy ahead for good.
Keane made it 3-1 with another penalty shot in stoppage after Dynamo goalkeeper Tally Hall was called for a hard foul in the penalty area.
The Galaxy bested Houston in the MLS Cup for the second straight season in David Beckham's final game with the club. They joined D.C. United as the only franchises with four league championships.
Calen Carr scored in the first half for the Dynamo.