General Manager Trent Baalke thanked Akers in a statement Wednesday, calling the kicker a "true professional who represented himself and this organization with class."
Akers appeared in all 32 regular-season games and five playoff contests the past two seasons. He connected on 73 of 94 field goal attempts and all 78 extra points.
In 2011, Akers set NFL records with 44 field goals made and 52 attempted. He also tied the league mark for the longest made when he kicked from 63 yards in last season's opener at Green Bay.
But Akers made just 29 of 44 attempts last season, his lowest percentage since 1999. The 49ers even brought in Billy Cundiff to compete against Akers before the divisional-round playoff and NFC championship game.