Raul Ibanez and Carlos Ruiz each had two RBIs to lead the Phillies to their fifth straight win.
Halladay (12-4) had trouble pitching in the heat and humidity in his last start at Chicago and left after four-plus innings. It was 94 degrees for the first pitch Sunday, and Halladay allowed three runs and eight hits and didn't get the side in order until the sixth.
He labored through the first five innings, then retired the last 10 batters.
Padres center fielder Chris Denorfia robbed Raul Ibanez of a home run with a leaping catch over the wall.
Halladay felt ill against the Cubs and had little explanation for why he was so affected by the heat. The temperature hit the mid-90s in the first when he gave up a quick run to the Padres.
Halladay gave up a pair of runs in the fourth that cut Philadelphia's lead to 5-3. That's the way it stayed the rest of the game because Halladay only got better the deeper he went. He fanned Kyle Phillips to end the fifth and didn't allow another runner. He threw 116 pitches and is tied for the NL lead in victories.
Antonio Bastardo worked a scoreless ninth for his eighth save and helped Philadelphia beat the Padres for a 10th straight time.
On the day senior adviser Pat Gillick went into the Baseball Hall of Fame, Philadelphia continued its push for a fifth straight NL East title.
Shane Victorino's RBI single and Ibanez's run-scoring double off Tim Stauffer (6-7) in the first made it 2-1. Ruiz added a two-RBI double in third for a 5-1 lead at the same time Gillick was giving his speech in Cooperstown, N.Y.
Stauffer allowed five runs and eight runs in 5 2-3 innings.
The Phillies nearly extended their lead in the seventh when Ibanez hit a shot to the 398-foot spot in center. Denorfia, in the game after Cameron Maybin left with a left hip flexor strain, sprinted with his back to home place. He twisted his body at the last second and extended his arm over the short wall to rob Ibanez.
Ibanez had a bitter look on his face as he rounded first.
Phillies fans recognized Denorfia's great catch with a nice ovation. Some fans even stood.
Fans can afford to be polite to the opposition this year the way the Phillies are rolling. The Phillies have won nine straight series and will go for a four-game sweep Monday.
Notes: Phillies RHP Roy Oswalt (back) is set to make a rehab start Wednesday at Triple-A Lehigh Valley. He said he felt good after a Sunday morning bullpen session. He hasn't pitched for the Phillies since the end of June. ... Phillies 3B Placido Polanco (back) fielders grounders and could be close to starting a rehab assignment. ... The Phillies have won each of Halladay's last nine starts at home. Halladay is 6-0 over that span. ... Ruiz has a 10-game hitting streak.