Webster broke his foot during the third quarter of last weekend's round-15 clash with Richmond at Etihad Stadium.
The 21-year-old Tasmanian made his AFL debut in 2013 and is averaging 15 disposals in 11 matches this season.
"He's going to be managed in a cast and won't be running for about 12 weeks," St Kilda team physio Andrew Wallis told the club's website.
"He is out for this year."
The Saints face 14th-placed Carlton at Etihad Stadium on Sunday.
Veteran St Kilda midfielder Lenny Hayes will have a fitness test for a groin injury.
The Saints have a 3-11 win-loss record after last week's ninth consecutive defeat.
