Phillies assistant general manager Scott Proefrock delivered the news before the Phillies played the New York Mets on Tuesday night.
Halladay was pulled from Sunday's start after just two innings. At the time, the team said the two-time Cy Young winner had shoulder soreness.
To fill his spot on the 25-man roster, catcher Erik Kratz has been recalled from triple-A Lehigh Valley.
Halladay, 35, has gone 4-5 with a 3.98 ERA in 11 starts this season. He threw only two innings in his last start on Sunday at St. Louis before being removed from the game due to right shoulder soreness.
Kratz, 31, has appeared in four games for the Phillies this season, mostly as a pinch-hitter. He has hit .250 with one home run and one RBI in 2012. This is the third recall of the season for Kratz, who will be available for tonight's game in New York.