Jay Heaps' men assured themselves of a top-three finish in the Eastern Conference in MLS thanks to the victory at BBVA Compass Stadium.
Giles Barnes had given the hosts, who were already out of play-off contention, a surprise first-half lead before Nguyen's second-half double.
The Revolution sit second in the East - three points adrift of leaders DC United - while the Dynamo are eighth.
Houston went ahead in the 37th minute as Barnes tucked away a rebound after Omar Cummings' fierce strike was parried by Revolution goalkeeper Bobby Shuttleworth.
Nguyen would make all the difference in the second half as he took his tally for the league season to 17 goals.
The equaliser came in the 65th minute after a well-worked move and good finish.
Jermaine Jones played fellow substitute Kevin Alston in behind down the left and the latter's cutback found Nguyen, who took a touch inside the area before curling his shot into the top corner.
A scrappy 87th-minute winner followed.
The Dynamo failed to clear their lines before Darrius Barnes touched a pass to Nguyen to tap in from close range and give the Revolution their win.
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