Henry scored his MLS-best ninth goal of the season when he corralled a ball sent his way from right back Connor Lade and gently lobbed it over Revolution goalkeeper Matt Reis for the tally.
The Red Bulls (4-3-1) rode Henry's goal to the win with the help of rookie goalie Ryan Meara, who made two late saves on New England's Benny Feilhaber to preserve the shutout.
New England (2-5-0) fell for the third straight game and sustained its fourth shutout loss.
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