Hoeft's last season in Major League Baseball was 1966, as he appeared in 36 games for the Cubs, before being released in August. In August, he was signed by the San Francisco Giants initially as a coach and batting practice pitcher before being activated in September when playing rosters increased to 40 men. He posted a 0–2 win-loss record in four games pitched during his second tour with the Giants, before announcing his retirement at the end of the 1966 season.