The 33-year-old did not play on Sunday but was penciled into the Giants lineup Tuesday before being a late scratch. An MRI test later revealed the break, which will leave Aoki in a cast for two weeks.
The move on Wednesday is retroactive to June 21.
Travis Ishikawa was called up from Triple-A Sacramento to take Aoki's roster spot. Ishikawa hit a three-run home run in the bottom of the ninth inning to win Game 5 of the NLCS for San Francisco last season.