The Belarussian now faces a race against time to be fit for the first grand slam of the season, which begins at Melbourne Park on Jan. 14, after the toe problem led to her late withdrawal from the clash against Williams.
She made the announcement about her withdrawal just 30 minutes before the match was scheduled to begin.
The Australian Open champion will not play another match before she opens the defence of her title and while the injury is to the big toe on her right foot, Azarenka expects to be fully fit for Melbourne.
"I am not concerned about that," she told reporters.
American world number three Williams will now meet either Russia's Anastasia Pavlyuchenkova or Ukraine's Lesia Tsurenko in the Brisbane final on Saturday. (Reporting by Will Swanton; Editing by John O'Brien)
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