It was Donovan's MLS-high eighth goal of the season, all coming in the last seven games.
''It's not a hundred percent chance to score, but it's pretty close,'' said Donovan, who has three penalty kick goals this season. ''There is a lot more that goes into a penalty than people realize. It's something that I work on and something I've gotten comfortable at over the years.''
The MLS-leading Galaxy (7-2-5) played without David Beckham, but had no problem controlling the action in improving to 4-0-2 at home. The shutout was the fifth of the season for Los Angeles.
''It's clicking right now,'' Galaxy defender Sean Franklin said. ''The whole team is playing well defensively.''
Houston (3-4-5) is winless in its last five matches. The Dynamo have dropped all six road contests this season.
''We've played pretty well on the road,'' Houston coach Dominic Kinnear said. ''I don't think we played very well tonight, but we we're still in the game. It's all about getting chances and taking those chances.''
Late in the first half, the Galaxy worked the ball up from their own end. It resulted in a long shot attempt by Chris Birchall that hit the arm of Houston midfielder Lovel Palmer in the box.
Donovan sent the penalty kick to the lower right corner as goalie Tally Hall went diving left.
Beckham is expected to rejoin the team prior to its match Saturday in New England. It will be the Galaxy's third contest in a span of eight days.
''I don't think you need to be a genius to figure this one out. This is real challenging,'' Galaxy coach Bruce Arena said. ''On top of it, we go across the country. This is not a good way to schedule. But it is what it is.''
Neither team was able to muster a shot on goal prior to Donovan's tally. But the Galaxy weren't hurting for chances, getting three promising looks before halftime.
The last of the opportunities saw Dynamo defender Hunter Freeman make a sliding save of the ball following a goal-line cross in front of an empty net with Donovan standing on the doorstep.
The Dynamo weren't able to crack the Galaxy defense, mustering just one shot on target
Houston midfielder Brad Davis made his club record 137th regular-season appearance.