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.
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