On the game-winning play, Watson used his chest to redirect a corner kick from Michel into the net on a set-piece, breaking a 1-1 tie.
Jackson also scored for MLS-leading FCD (7-1-3), which reeled off its ninth game without a loss.
Dwayne De Rosario scored in the 44th minute for United, which tumbled to a league-worst mark of 1-8-1.
Notable deaths of 2014 [PHOTOS]
Michael Sam cut from the Dallas Cowboys