Pacioretty appeared to be blindsided by Stoner, who drove him into the boards deep in Anaheim's end after Pacioretty tried to pass the puck back to the point as a Montreal power play expired early in the third period.
No penalty was called on the play, but the Canadiens' Brandon Prust later fought Stoner.
Pacioretty stayed down for a time, was helped off the ice, and did not return.
He was taken to hospital as a precautionary measure, said the Canadiens, who didn't elaborate on the extent of his injury.
"I think their team wasn't happy about it," Stoner said after Anaheim's 2-1 win. "I didn't mean to hurt him but the game's fast and sometimes guys go into the boards wrong, so I hope he's all right and I didn't mean any intentions to hurt him."
Pacioretty leads the Canadiens in goals (13) and points (25) through 33 games this season.