The 27-year-old Boone reached agreement on a restructured $6 million, two-year contract Sunday. The 49ers requested a roster exemption and Boone must be added to the 53-man roster before he can play.
As part of his new deal, fines for missing the mandatory minicamp and training camp were waived.
Boone is a key member of a veteran offensive line and the unit struggled to protect quarterback Colin Kaepernick during the preseason. Boone has started every game the past two seasons.
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