Carlisle, 20, was pursuing Carlton's Levi Casboult as the forward went on a long lead about 19 minutes into the third quarter and collapsed to the ground as the Blue was met heavily by Stewart Crameri.
Carlisle lay on the ground until he was assisted by trainers, who assessed his left ankle, before carrying him from the field. He received further treatment on the bench before disappearing down the race.
The Bombers, who lost Dustin Fletcher to a groin injury in the first quarter, trailed Carlton by 79 points at three-quarter time.
Fletcher, 37, stretched out to brilliantly spoil Eddie Betts as he attempted to mark in front of goals at the Punt Road end 13 minutes into the first quarter, but was seen grimacing in pain with hands on knees shortly after.
He soon left the ground, copping solid bumps from Mitch Robinson and Zach Tuohy on the way, and went down the race for treatment.
He appeared some minutes later, but was handed the red vest with substitute Leroy Jetta taking his place on the ground.
