He will have the operation Wednesday.
Bernier missed five games in March due to the injury.
He then aggravated the problem April 3 against the Boston Bruins and finished the season on the sidelines.
Bernier was 26-19-7 with a 2.68 goals-against average and a .923 save percentage this season.
The Leafs missed the playoffs after posting a dismal 6-14-2 record down the stretch.
The injury likely means Canada will not be able to call on Bernier for next month's world hockey championship in Belarus.