A calamitous error from Dynamo goalkeeper Tyler Deric handed the visitors three points at BBVA Compass Stadium in Texas, while Orlando substitute Pedro Ribeiro also deserved credit for his pressure.
Ribeiro's pressing forced a back-pass to Deric, whose first touch set up a 50-50 opportunity on the edge of Houston's defensive penalty area.
Both players reached the ball at the same time but Ribeiro's challenge was stronger, as the ball looped high towards goal.
Ribeiro got ahead of Deric and held front position as he attempted to shepherd the ball home, and when it came down the Houston gloveman could only punch it into his own net.
It capped off an impressive performance by Orlando - who were held 1-1 at home by New York City in their MLS debut last week - as they just edged possession in Houston, while denying Dynamo a shot on target for the entire 90 minutes.
Houston had six corners to just three from the visitors but Orlando made two blocks and 30 clearances to ensure keeper Donovan Ricketts did not have to make a save.
The win takes Orlando to the top of the Eastern Conference with four points, although Adrian Heath's men could be overhauled over the course of the weekend.
