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.
Also Monday, the team signed cornerback Chance Casey, tackle John Fullington and running back Kendall Gaskins to the practice squad.