Lee had received the contract Monday after trying out last weekend at the 49ers' rookie minicamp, where he caught passes from rookie quarterback Trey Lance on Friday during the portion of practice open to the media.
The 29-year-old wide receiver opted out of the 2020 season due to the coronavirus pandemic after signing with the New England Patriots as a free agent. The Patriots released him in March.
Lee, a 2014 second-round pick by the Jacksonville Jaguars, has 174 catches for 2,184 yards and eight touchdowns in 59 career games.
In a related move, the 49ers signed wide receiver Bennie Fowler to a one-year contract. Fowler, a six-year veteran, spent the 2020 season with the New Orleans Saints, catching two passes for 11 yards.