The classy left footer, who has become a key component of St Kilda's defensive structure in 2014, broke his foot during the third quarter on Saturday.
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The injury is a bitter blow for the Saints, who are likely to be without fellow defender Jarryn Geary for the remainder of the year with a broken arm.
Webster will not be able to commence running again for another three months, according to St Kilda Head Physio Andrew Wallis.
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In other injury news, Lenny Hayes, Arryn Siposs, Spencer White and Sam Fisher will all undergo tests this week to determine their availability for the upcoming round of games, while Sam Gilbert is just a month away from a return to action.
Click here for the full Round 15 Injury List.