The deal is reportedly worth up to $18 million with $10 million guaranteed.
The Niners acquired Tomlinson in a trade with the Detroit Lions just prior to the start of the 2017 regular season for a 2019 fifth-round draft pick.
In his first season with the 49ers, Tomlinson started 15 games and performed admirably.
He was originally selected by Detroit with the No. 28 overall pick in the 2015 NFL draft out of Duke.
Tomlinson started 24 games over his first two NFL campaigns, and he has primarily appeared at left guard throughout his career.
He had been set to enter the final year of his contract in 2018 since the Niners declined his fifth-year option for 2019.
Tomlinson is expected to serve as the starting left guard this season and a primary protector of quarterback Jimmy Garoppolo with another former first-round pick in Jonathan Cooper backing him up.