The Union drew first blood in the 34th minute when Jack McInerney played a cross into the box that Gomez collected and fired past TFC goalkeeper Milos Kocic thanks to a deflection.
Philadelphia doubled its advantage 2 minutes later. Adu latched onto a through-ball from Gabriel Farfan on the left side of the box and put a shot past Kocic from a tough angle.
Antoine Hoppenot also scored for the Union (5-9-2), who are seeking to make a late playoff push.
Last-place Toronto fell to 2-11-4.