Boone will land a new two-year deal to replace his old contract, with an increase in salary and incentives if he reaches the Pro Bowl, according to sources.
The 49ers also will not be able to use their franchise tag on Boone once the new contract has expired, sources said.
Boone originally was scheduled to make up to $4 million over the next two seasons under his previous deal, sources said.
The 27-year-old Boone also racked up $1.2 million in fines during his holdout. Sources declined to comment how those fines would be handled or whether they would be worked into Boone's new deal.
The 6-foot-7, 330-pound Boone has started every game for the 49ers over the past two seasons.