On the play, Chris Tierney found Fagundez behind the Toronto defense with a pinpoint cross and the Revs midfielder slotted it home for his third goal in three games.
Juan Agudelo added a stoppage-time goal for New England (4-4-4).
TFC (1-7-4), meanwhile, lost for a fifth straight time while stretching its overall winless streak to nine contests.
Notable deaths of 2014 [PHOTOS]
Arizona Cardinals player formally charged