Williams, who was scheduled to undergo surgery on the ankle, was injured on by a block by J.R. Sweezy early in the 49ers' 29-3 loss to the Seattle Seahawks on Sunday.
Williams, a three-year veteran who made his first career start against the Seahawks, has played in six games and has 11 tackles. He originally joined the team as an undrafted free agent out of Notre Dame in 2011.
The 49ers also signed fullback Owen Marecic to a one-year contact on Tuesday.
Marecic played for 49ers coach Jim Harbaugh at Stanford.
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