Shane Victorino homered and scored the go-ahead run on Jayson Werth's two-out, bases-loaded walk against Mat Latos in the fifth.
Halladay (8-3) allowed 10 hits and walked one, but held San Diego to two runs in his first game since his gem at Florida last Saturday. The right-hander received a standing ovation from the sellout crowd of 45,080 as he walked in from the bullpen.
Jose Contreras and J.C. Romero combined to pitch the eighth, and Brad Lidge tossed a perfect ninth inning for his second save.
Latos (5-4) issued a season-high four walks in five innings, yielding three runs and four hits. The righty entered with a 1.29 ERA in his previous five outings.
The Phillies managed only five hits and struck out 11 times. They were coming off a 2-7 trip to NL East rivals New York, Florida and Atlanta.
Halladay singled with one out in the third and scored on Victorino's homer to right field.
Tony Gwynn Jr. hit an RBI single in the second and Adrian Gonzalez added a sacrifice fly in the fifth for NL West-leading San Diego, which lost right fielder Will Venable in the fifth inning when he jammed his neck sliding into third. He was replaced by Chris Denorfia.
Halladay singled with one out in the third and scored on Victorino's ninth homer.
Umpire Jim Joyce, whose blown call at first base cost Detroit pitcher Armando Galarraga a perfect game on Wednesday, was at third for the first game of the series. He was greeted with a smattering of boos during pregame introductions.
NOTES: Phillies LHP J.A. Happ (left forearm strain) pitched two innings in an extended spring training game, throwing 28 pitches. General manager Ruben Amaro Jr. said Happ felt "comfortable," and is scheduled to pitch three innings for Single-A Clearwater on Tuesday. ... Phillies reliever Ryan Madson (broken right big toe) had the walking boot removed from his foot. ... Phillies SS Jimmy Rollins (strained right calf) took batting practice. ... San Diego reinstated C Yorvit Torrealba from the restricted list, and optioned Dusty Ryan to Triple-A Portland. ... Padres SS Everth Cabrera, (strained hamstring), took grounders before the game.
