The fourth-year right tackle will join the 49ers on a one-year, $2.2 million deal with $1.4 million guaranteed. Because the Seahawks tendered Gilliam at the lowest level, they will not receive any draft pick compensation from the 49ers, who had signed Gilliam to the offer sheet on Monday.
Seattle had five days to match the offer but made their decision just a day later.
Gilliam started 29 games over the past two seasons for the Seahawks. The team will now likely move 2016 first-round pick Germain Ifedi from right guard to right tackle. Seattle could also explore options in the draft to replace Gilliam.
San Francisco previously offered Gilliam a multiyear deal, which he turned down. A one-year contract allows him to test unrestricted free agency next offseason at the age of 27.
Gilliam originally signed with the Seahawks as an undrafted free agent out of Penn State in 2014.