Halladay said he will likely meet with doctors on Tuesday, and does not anticipate needing an MRI.
Halladay said he first felt the pain in the back his shoulder halfway through his last start, a loss against the Nationals on Tuesday. 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) was pinch-hit for in the third with Philadelphia (25-24) trailing, 4-0, after throwing 36 pitches. He 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.
Halladay has struggled this season, especially this month. The two-time Cy Young Award winner is 1-3 with 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.
Joe Savery and Chad Qualls struggled in relief for the Phils. Savery gave up two runs on four hits in two-plus innings. Qualls gave up a pair of deep homers in two innings -- a three-run blast to Carlos Beltran in the fifth, and a solo shot to rookie Matt Adams in the sixth.
St. Louis starter Adam Wainwright kept the Phillies' offense in check for six innings. The right-hander allowed seven hits, including an RBI single by Juan Pierre in the third.
"He looked like he was trying to stay away, move the pitches around to keep you guessing," Mike Fontenot said of Wainwright.
The Phillies added a run in the eighth off St. Louis reliever Victor Marte. The inning began with a pair of singles, but was cut short due to fine defensive plays by Rafael Furcal at short and Daniel Descalso at second.
The Phils scored once more in the ninth, collecting a pair of hits off rookie reliever Chuckie Fick. But Michell Boggs came in with two outs and closed the door.
Continuing an unfortunate trend this season, the Phillies are 5-14 when their opponents score first. They are 3-16 when trailing after six innings, and haven't won a game this season when trailing after the seventh.