Halladay surrendered the fifth grand slam of his career to Cardinals catcher Yadier Molina in the first inning, but worked a perfect second getting groundouts from pitcher Adam Wainwright, Rafael Furcal and Skip Schumaker.
The two-time Cy Young winner pitched with the injury the last few innings of his last start, and cutting back on throwing between outings didn't help.
"Worried? Yeah, definitely, I'm concerned," Phillies manager Charlie Manuel said after the Phillies fell 8-3 in their bid for their first four-game sweep in St. Louis in 99 years. "Pitching is one of the big things on our club and when guys miss a turn, it concerns me."
Manuel declined to lay out a scenario if Halladay can't make his next start or worse, saying only: "If we have to fill a rotation spot, we'll get somebody and fill it. The games will go on."
Asked about his level of concern, pitching coach Rich Dubee said: "I don't know. I'm not a doctor."
Dubee told Halladay (4-5) that his day was done in the dugout after chatting with the pitcher.
"I know he's had a cranky shoulder and he hasn't looked right, and didn't look right today," Dubee said. "And I knew he wasn't going to come out of the game, so I basically said 'That's enough.' "
Halladay said the soreness comes from the back of the shoulder. He anticipates an examination on Tuesday.
"I'm hoping it's something we can just calm down quickly and get back out there," the pitcher said. "It's not the point where I'm in agony throwing pitches."
Halladay departed with a 3.98 ERA after an outing that matched the second-shortest outing of his career.
Halladay was 19-6 with a 2.35 ERA last year, and allowed 10 homers in 32 starts. Since winning his first three starts, Halladay is 1-5 with a 5.08 ERA in eight games, and the Phillies have lost seven of his last eight starts.
He's absorbed the last two losses for the Phillies, who entered the series finale on a four-game winning streak.
Molina's third career grand slam was the fifth allowed by Halladay, two of them this year after the Braves' Brian McCann connected May 2 at Atlanta. Halladay has allowed six homers this season, all this month.
Unlike 2004, when Halladay had two stints on the 15-day disabled list with a shoulder injury, he wasn't able to pinpoint a particular pitch with which the pain began. The biggest problem is the time between innings when the shoulder tightens.
"It's kind of that down time when it seemed to come up," Halladay said. "I think if I just went out and threw 100 straight pitches without taking a break it might be all right."
Cardinals manager Mike Matheny caught Halladay as a rookie in 1999 in Toronto, and knew the pitcher was off his game.
"You just didn't know if it was physical or if it was just one of those things where he couldn't get anything positive going," Matheny said. "But usually you can tell if something isn't completely right.
"Those guys aren't squaring him up like they have been lately."
Information from The Associated Press was used in this report.