Josh Johnson signed a two-year deal with the New York Giants, his agent announced on Friday morning.
Johnson played for Jim Harbaugh at the University of San Diego, and the two reunited with the 49ers in 2012 and 2014.
The 30-year old quarterback never appeared in a regular season game for San Francisco.
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He entered the NFL as a fifth round pick of the Buccaneers in 2008.
Johnson was active for two games with the Giants last season, as the backup to Eli Manning.
Over his career, Johnson has seen regular season action in 29 games and is 0-5 as a starter.