Bernier revealed the injury, one that first occurred at the team's morning skate, after the Maple Leafs' 3-2 win against the Ottawa Senators on Thursday, one that he left after the first period.
Bernier is expected back Saturday.
"Bernier has an irritation on his knee from some new equipment he’s wearing, part and parcel to the equipment change," Carlyle said. "I guess the under-kneepads are new and they irritated the top of his knee cap. It's what we're dealing with.
"I really haven't got a true explanation of why or how that happened. We're doing what's necessary to fix it."
Competing for the starting job with James Reimer, Bernier stopped 11 of 12 shots in 20 minutes. The 25-year-old was acquired from the Los Angeles Kings in a June trade for forward Matt Frattin, goalie Ben Scrivens, and a second-round draft pick in either 2014 or 2015.
Nazem Kadri did practice Friday, centering a line with Joffrey Lupul and David Clarkson after he left the game Thursday with a bruised hand sustained when he blocked a shot. X-rays taken after the game were negative and Kadri skated without a wrap on his hand.
"It's a little sore, a little sensitive," Kadri said. "It's my bottom hand on my stick, where I'm leaning on it the most."
Colton Orr (leg bruise) continued to work out on his own, while Lupul (back spasms) practiced Friday and could play Saturday in Buffalo.
"He looked good out there," Carlyle said. "He didn't leave [practice] early. So I would say he's progressing. He's an option for us starting [Saturday]."