Bernier's left knee appeared to bend awkwardly after Paul Ranger pushed Bruins centre Patrice Bergeron into him. The Leafs' starting goaltender remained down on the ice in pain before he was forced to leave the game.
Backup James Reimer began stretching immediately when Bernier was injured and entered at the 7:22 mark of the third period.
Bernier missed five straight games in March with a groin injury. This was his fifth straight game since returning from that absence.
The Leafs led the Bruins 3-2 when Bernier left the game. He stopped 25 of the 27 shots he faced.