The hosts should have been ahead in the ninth minute when Lee Nguyen raided down the right and put a lovely ball across the face of goal, but Kelyn Rowe somehow managed to fire over from yards out.
Philadelphia almost made the home side pay for their missed chances when Michael Farfan found space in the box, but his effort was well saved by Bobby Shuttleworth, who tipped his shot over the bar.
After the break, New England finally took the lead when Fagundez fired in from close range following a lovely move down the right involving Nguyen and Rowe.
The Revolution doubled their lead soon after, as Nguyen found the net after Saer Sene's shot was saved by MacMath but the midfielder was there to fire in the rebound.
Union striker Jack McInerney had a late chance to get his side a goal back but he was denied by a great save by Shuttleworth, who tipped the ball round the post, which was enough to secure the win for his side.