"You have this stuff from time to time, and most times, if you take care of it, it kind of goes away," Halladay said after the 8-3 loss. "But it never seemed to go away. It was there basically throughout the game."
Halladay said he will likely meet with doctors on Tuesday, but does not anticipate needing an MRI.
Halladay said he first felt the pain in the back of his shoulder halfway through his last start, a loss against the Nationals on Tuesday. Halladay went six innings against Washington, allowing five runs on nine hits. The 6-foot-6 right-hander said everything checked out fine after that game. He added his shoulder felt strong this week, but he cut back on throwing just to be careful.
Halladay (4-5) allowed a two-out grand slam to Yadier Molina after loading the bases on two singles and a walk in the first inning. Halladay shut down the Cards in order in the second, inducing three groundouts.
He was done after allowing four runs on four hits with a walk and no strikeouts.
Phillies pitching coach Rich Dubee asked Halladay how he felt after the second inning, and when Halladay told Dubee he was still feeling pain, Dubee made the call to end his day early.
"I didn't want to say anything," Halladay said. "I think it was the right call. It's hard for any pitcher to come and tell their coach they need to come out. I don't know if I would have done that. I probably would have kept going."
"I know he's had a cranky shoulder, and he hasn't looked right," Dubee said. "[He] didn't look right today, and I knew he wasn't going to come out of the game. So I basically said that was enough."
The outing was Halladay's shortest since he exited after four innings in Chicago against the Cubs on July 18 of last season. Halladay left that game due to heat exhaustion.
"He's had such a dominant career," Cardinals manager Mike Matheny said of Halladay. "I was fortunate to catch him his rookie year and watched him develop in this game, and I've always had the utmost respect for how he's gone about it. He's a class act as well as a very good pitcher. You know that guys are going to struggle sooner or later. You're going to have those seasons. He hasn't had many of them since he was very young in his career. ... Usually, you can tell if something isn't completely right because guys aren't squaring him up like they have been lately."
The two-time Cy Young Award winner has struggled this season, especially this month. Halladay has a 6.11 ERA in May with 24 earned runs over 35 1/3 innings in six starts. Halladay was 3-2 with a 1.95 ERA in five starts in April.
Halladay has had shoulder issues before. He missed two months of the season and was limited to 133 innings in 2004 due to a right shoulder strain. Halladay said what he's feeling now is not the same kind of pain. That season, each start from the first inning to the last was painful.
"That's not the case right now," Halladay said. "I really was fighting it back then. I'm hoping it's something we can just calm down quickly and get back out there."
Halladay is unsure whether he'll be available for his next start, and will wait to hear from doctors before making any decisions. Phillies manager Charlie Manuel said he is "definitely concerned," though.
However, Manuel isn't ready to start thinking about replacing Halladay in the rotation just yet.
"If we have to fill a rotation spot, we'll get somebody to fill it," Manuel said. "The games will go on. I've been in this game a long time. I hate to see players get hurt, probably more than you'd ever realized. But at the same time, it moves on. You have to."
Mike Still is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.