"I was a little surprised" he cleared waivers, manager Bruce Bochy said. "I didn't know what would happen. I thought there was a good chance we would lose him."
Ishikawa's walk-off, three-run home run against the Cardinals in the National League Championship Series last year advanced the Giants to the World Series, where they would eventually beat the Royals.
Ishikawa was designated for assignment May 25 after being reinstated off the 15-day disabled list. He opened the season with a back injury and had not played with the big league club in 2015.
The Giants ran out of room on their 25-man roster and both in the outfield and at first base in terms of playing time, prompting the designation.
"I'm happy for the fact that he gets to stay with us [in the organization]," Bochy said. "You feel terrible that it hasn't worked out to where he's here [in San Francisco]. But the fact that he is going to stay is nice to know."
• Former Giant and Bay Area native Kevin Frandsen signed a Minor League contract with San Francisco and is heading to Triple-A Sacramento, the team confirmed Sunday. The D-backs released the 33-year-old utility infielder Saturday. He last appeared in the big leagues in 2014, playing in 105 games for the Nationals.