Through eight shutout innings, Halladay (2-0) allowed only a pair of singles by Adam LaRoche, who talked his way back into Washington's lineup despite a hurt groin. In the ninth, Halladay allowed four hits, including RBI singles by Laynce Nix and Danny Espinosa.
With two on, the two-time Cy Young Award winner ended the game by throwing six strikes in a row to fan pinch-hitter Matt Stairs and Ivan Rodriguez, who argued the game-ending call at length.
Halladay had nine strikeouts and two walks.
John Lannan (1-1) is 0-9 against Philadelphia.