Boone passed his physical and rejoined the team on Monday, the team announced.
NFL Media Insider Ian Rapoport reported that the Niners ended the lengthy standoff by rolling Boone's incentives into his base salary. Boone can now make $6 million in salary over the next two years. Before the deal was reworked, Boone was scheduled to make $3.7 million in salary. He can earn $8 million if he earns All-Pro nods in both seasons.
Boone, 27, has been a rock on Jim Harbaugh's offensive line, starting 38 straight games over the past two seasons. With trouble on other fronts, this is a headache the organization is glad to be rid of.