There was no immediate word on the extent of Hutchison's injury; additional information is expected to be available on Saturday following a series of tests.
Hutchison became the third Blue Jays starter in the past four games to have his outing cut short because of an injury.
"I've never seen it three out of four days," manager John Farrell said while in a state of near-disbelief. "As soon as you say 'never,' or [that] you've not seen something in this game, then it kind of rears its head. It's unfortunate for Drew, for us, for all involved.
"We're getting challenges thrown at us from every different angle, and health right now is certainly the main one."
Hutchison began the start against Philadelphia by retiring the first two batters. He then worked the count to 1-1 against outfielder Hunter Pence before throwing what would end up being his final pitch of the night.
The 21-year-old immediately called for trainer Hap Hudson after feeling something in his elbow, and Farrell removed him from the game after a very brief meeting on the mound.
It's not clear how severe the injury is, but whenever it involves the pitching elbow, it becomes dangerous territory.
"I think any time a pitcher calls the training staff to the mound, something's not right," Farrell said of Hutchison, who is 5-3 with a 4.60 ERA in 11 starts. "What's fresh in everyone's minds is two of the last three days, when the starters had to come out of the game.
"I'm not saying Drew's feeling the worst, but when you feel that kind of discomfort, he's obviously concerned, as we all are."
The injury could not have come at a worse time. Right-hander Brandon Morrow left his start on Monday with a strained left oblique, and two days later, Kyle Drabek was forced to depart with a tear in his ulnar collateral ligament.
A timetable for Morrow has yet to be established; Drabek is set to visit Dr. James Andrews on Monday, and he could be in line for his second Tommy John surgery.
Toronto ended up winning Friday's game against Philadelphia, 3-0, but the result took a backseat to the current state of affairs.
"It was not good, because we lost another starter," right-hander Carlos Villanueva said after throwing four scoreless innings in relief. "The result of the game, whatever. We won, I'm happy about that, but obviously we're concerned for Hutch."