The game was delayed for 55 minutes by rain.
After he allowed a first-inning leadoff homer to Will Venable, Halladay settled down before he unraveled in the fifth.
That's when Halladay issued four straight one-out walks, the first time he has done that in his career. Then he overthrew first base on what was ruled an infield single to Tommy Medica, and two runs scored.
Halladay departed with a 7-4 lead after 41/3 innings. Justin De Fratus allowed a sacrifice fly to Mark Kotsay, scoring the fifth run, before getting the final out.
Halladay allowed five runs on four hits. He walked five and struck out six. He also walked five in his last start, a no-decision during a 3-2 loss to Washington on Sept. 4.
Against the Padres, Halladay threw 101 pitches, 57 for strikes.
"Each time out, I feel things are improving, but it seems like I have a situation or two where I have to overcome it," Halladay said. "I want to be out there and want to pitch and feel I owe it to the organization and team, and feel healthy for the first time in 21/2 years. And I know it's asking a lot, but I want to be better than what I am showing, and I feel like I am."
He was successful earlier in the game as the Padres chased balls out of the strike zone, but by the fifth, San Diego showed plate discipline and it helped end Halladay's evening.
With a fastball in the 88-m.p.h. range, Halladay continued to rely on his curveball and change-up. He had success with both pitches until the fateful fifth inning.
Halladay has pitched four times since returning from surgery. His ERA in those games is 5.07.
"It could be a little rust and a little bit mechanics at this stage," interim manager Ryne Sandberg said of Halladay. "His command is not where he wants it to be, but his health is fine and his velocity is staying about the same."
Venable's leadoff homer was the Padres right fielder's 22d of the season. Halladay needed 21 pitches in the first inning. After allowing one run, his ERA in 11 starts during the first inning is 13.09.
Halladay's opening-inning issues were minor compared with Padres righthander Tyson Ross, who allowed six earned runs in the first and was yanked after two-thirds of an inning.
The big hits were two-run doubles by Carlos Ruiz and Cesar Hernandez. The inning ended on Hernandez's double when Halladay, who had drawn a bases-loaded walk, was easily thrown out at the plate.
That type of offense was surely appreciated by one of the more noted spectators, Eagles quarterback Michael Vick.
Halladay was supposed to start on Tuesday, but he got the flu last Friday and was pushed back two days.
Contact Marc Narducci
at firstname.lastname@example.org. Follow @sjnard on Twitter.