NFL.com reported that the Niners have agreed to increase Boone's base salary over the final two years of his contract. The fifth-year lineman will now earn $6 million with an additional $2 million in incentives over the life of the deal.
Boone had been slated to make $3.7 million between 2014 and 2015 on the four- year extension he signed near the end of the 2011 season.
The 49ers later announced that Boone passed a physical. The team will request a roster exemption with him unlikely to be ready for San Francisco's regular- season opener at Dallas this Sunday.
Boone has started all 32 games at right guard for San Francisco over the past two seasons and emerged as a key part of an offensive line that has helped the 49ers to back-to-back NFC Championship games as well as a Super Bowl appearance.