Woods underwent surgery to repair the damaged thumb on Monday after being inactive for San Francisco's first three games.
The injury is the latest problem in what has been a disappointing early career for Woods, a first-round (31st overall) selection by the 49ers in the 2004 draft. He had just seven catches as a rookie and was fourth on the team's depth chart this season, behind Brandon Lloyd, Arnaz Battle and Johnnie Morton.
Woods is the second receiver to be placed on IR by the 49ers this season. Tight end Eric Johnson is also out for the year with a torn ligament in his foot.
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