Halladay, a right-handed starter, was charged with nine runs on four hits and four walks in 2 1/3 innings Sunday against Miami. After the game, he said he had been having shoulder problems since April 25.
Halladay, who turns 37 this month, was to travel to Los Angeles for further examination.
He is 2-4 this season with an 8.65 earned run average. Over a 16-year career with Toronto (12 years) and Philadelphia, Halladay is 201-104 with a 3.37 ERA. He won the Cy Young Award after the 2003 season with Toronto, when he was 22-7, and in 2010, when he was 21-10 for the Phillies.
Left-hander Joe Savery was recalled from Triple-A Lehigh Valley to take Halladay's spot in the roster. Savery is a reliever and Halladay's next starting assignment was to be Friday. The team hasn't announced who will take Halladay's place in the pitching rotation.