After getting a pass from Clyde Simms, Fagundez threaded his way into the penalty box and put a shot past Dynamo goalkeeper Tally Hall to break a scoreless tie.
Houston's Ricardo Clark scored an own-goal in the 84th, sealing the win for the Revolution (3-4-4).
The Dynamo, whose 36-game home unbeaten streak was snapped last week, dropped to 6-4-2.
Chipotle plans first price increase in 3 years
Justin Bieber crashes Drake Bell's album release party