The game was open from the start, with the action coming at both ends. New England came close to opening the scoring after just seven minutes when Fagundez fired over the bar from close range, before Philadelphia's Tranquillo Barnetta found himself in space before edging a shot wide.
Fagundez had another chance to open the scoring for the visitors soon after, but his effort found Andre Blake in the Philadelphia goal, before Barnetta tested Bobby Shuttleworth with a low shot at the other end.
Shuttleworth was called into action again before half time, as the American keeper was forced into a good save by Sebastien Le Toux.
The Revolution took the lead soon after the break, as Fagundez hit a low shot from 18 yards to find the back of the net.
Lee Nguyen came close to doubling the visitors' lead on 68 minutes after creating some space for himself, but his shot went straight into the arms of Blake, before the midfielder forced Blake into a crucial finger-tip save soon afterwards.
Fernando Aristeguieta came close to a late equaliser for Philadelphia, but his effort went over the bar.