Halladay arrived at Rogers Centre on Friday looking pale and complaining of pain in his lower right abdomen. Trainer George Poulis recognized the symptoms and took Halladay to a local hospital for surgery.
Halladay was placed on the 15-day disabled list. The Blue Jays did not immediately announce a roster move.
"You've got to look at it as a chance for someone else to step up," Blue Jays general manager J.P. Ricciardi said. "We're not going to sit here and raise the white flag, say we're quitting."
"We've got some young kids who are going to get an opportunity now. We'll see who can handle coming up here and giving us those innings, giving us a chance to win."
Halladay lasted only five innings and was hit hard in an 8-0 loss to Boston on Thursday, one start after giving up a season-high nine runs in an 11-4 loss to Texas. The 2003 AL Cy Young Award winner is 4-2 with a 4.37 ERA in eight starts.
The rout by Boston was the Blue Jays' ninth straight loss and left them in last place in the AL East.
On Thursday, Toronto lost closer B.J. Ryan for the year after he had ligament replacement surgery on his left elbow, and put right-hander Victor Zambrano on the 15-day disabled list with a strained right forearm.