The only goal of the game at the PPL Park in Chester, Pennsylvania came in the 75th minute. Jack McInerney headed Sebastien Le Toux's corner towards goal and after it was saved by visiting goalkeeper Bobby Shuttleworth, he tucked in the rebound.
It was McInerney's fourth winner against New England in six appearances.
New England could have restored parity almost immediately had Juan Carlos Toja not dragged his shot wide with only Zac MacMath to beat.
The win sees Union move up to second in the Eastern Conference, while their visitors are now seventh.