The Dynamo clinched the East's second seed and will face the Philadelphia Union in the semi-finals to open their play-off run
Adam Moffat, Bobby Boswell and Carlo Costly scored for Houston, while youngster Jack McBean netted a consolation for LA, who rested all of their 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 go on to assist the next goal shortly after half-time.
In the 48th minute, Houston extended their lead to 2-0 with a low shot from Boswell.
Costly put the game away in the 74th minute when he headed in a 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 deny the hosts a clean sheet.
The Dynamo end their season with 49 points and will face the Philadelphia Union in the semi-finals on Oct. 29. The Galaxy, meanwhile, will take on the lowest wildcard seed in the final four.