Halladay (1-2) recorded his first victory of the season and became the 109th pitcher in major league history to get 200 wins. The two-time Cy Young Award winner yielded five hits, issued one walk and struck out two.
Nix, pinch-hitting for Halladay in the ninth inning, bashed a one-out pitch from Jon Rauch (0-2) into the second deck in right field to break a 1-1 deadlock.
Michael Young provided an RBI for the Phillies, who took the rubber match of a three-game road series.
Marlins starter Kevin Slowey held Philadelphia to one run on nine hits over 5 1/3 frames in the no-decision.
Chris Valaika drove in Miami's only run.