The Dynamo clinched the East's second seed and will face the Philadelphia Union in the semifinals to open their playoff run.
Adam Moffat, Bobby Boswell and Carlo Costly scored for Houston. Youngster Jack McBean scored for LA, which rested all of its regular starters except goalkeeper Donovan Ricketts having already clinched the Supporters' Shield.
Moffat started the scoring with a long strike that made its way past Ricketts into the top corner of the net. Moffat would assist the next goal shortly after halftime.
In the 48th minute, Houston extended its lead to two with a low shot from Boswell.
Costly put the game away in the 74th minute. He scored on a header off a nice cross from Brad Davis, who finished the year with a league-leading 16 assists.
Making his MLS debut, McBean, at just 16 years old, was able to sneak one into Houston's net in the 88th minute to prevent the shutout.
The Dynamo end their season with 49 points and will face the Philadelphia Union in the semifinals on Oct. 29. The Galaxy, meanwhile, will face the lowest wildcard seed in the semis.