A play-off place in MLS already secured, Philadelphia extended its unbeaten run to four games.
Andrew Farrell's own goal was followed by Anthony Fontana's strike and the Union moved within three points of Toronto despite Tajon Buchanan's 80th-minute effort for New England.
Farrell turned a cross into his own net to give Philadelphia the lead in the first half before Fontana lobbed New England goalkeeper Matt Turner following a Jamiro pass in the 69th minute.
Fontana has scored four of his eight MLS goals for Philadelphia against New England, as per Opta.
Buchanan produced a wonderful strike from 20 yards to give the Revolution hope, but Philadelphia held on.