Patrick Mullins should have put New England ahead early on at the BBVA Compass Stadium, but he could only fire wide from a tight angle after forcing his way into the box.
Despite heading into the game as the firm favourites, the Revolution were soon forced onto the back foot as Houston quickly improved in the first half.
New England responded well after the break, and twice came close to levelling the scores when Steve Neumann and Charlie Davies struck wide from close range.
The equaliser would arrive in the 65th minute when Nguyen earned himself space inside the box before curling an unstoppable strike past Tyler Deric.
Neither side would take a backward step in the closing stages as they went in search for a late winner, and it was New England who clinched the points with three minutes of normal time remaining.