The Saints have also suspended Winmar from the club's Hall of Fame on Wednesday, following the 60-year-old's conviction on three charges of unlawful and common assault in the Bendigo Magistrates' Court.
The charges related to the allegations Winmar grabbed a woman by the arm, dragged her by the hair and hit her head against a door.
A statue of Winmar's stand against racism - which depicts the iconic 1993 moment where the St Kilda player lifted his jumper and pointed at his skin - at Perth's Optus Stadium was torn down under a directive from the West Australian government.
AFL Commission chairman Craig Drummond said Winmar's recent conviction rendered his place in Australian football as "inappropriate".
Winmar was inducted into the Hall of Fame in 2022 after a 251-game career with the Saints and Western Bulldogs, becoming the first Indigenous footballer to play 200 games in the AFL.
His stand in 1993 was pivotal in forcing the AFL to establish the racial and religious vilification rule in 1995 - a contribution Drummond acknowledged.
"The Commission acknowledges Nicky Winmar's significant contribution to Australian Football and his place in our history," Drummond said in an AFL statement.
"However, the recent findings against him render inappropriate his place in the Australian Football Hall of Fame.
"Violence against women has no place. Not in our community, not in our game, and not in the values the Australian Football Hall of Fame seeks to uphold.
"The Australian Football Hall of Fame exists to recognise the highest achievements in our game and admission to it is one of the greatest honours Australian football can bestow.
"The Commission has a responsibility to protect the integrity and reputation of that honour."
Winmar's Hall of Fame status at St Kilda will be determined after the legal process - which includes any possible appeals - is formally concluded.
He is not the first AFL player stripped of his Hall of Fame status.
In 2023, former North Melbourne, Perth and East Perth champion Barry Cable's "Legend'' status was revoked after a civil trial found he had sexually abused a young girl during his playing career.In April this year, Cable was acquitted of historical sexual abuse charges in a criminal trial.
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