The move comes 11 days after Story left a game against Baltimore because of a bruised left heel.
Boston made the move retroactive to Monday and recalled first baseman/third baseman Bobby Dalbec from Triple-A Worcester.
The 29-year-old Story, a two-time All-Star, is hitting .238 with 16 homers and 66 RBIs after leaving Colorado and signing a $140 million, six-year contract with the Red Sox. He switched from shortstop to second with Boston.
He was on the injured list from July 16 to Aug. 27 because of a hairline fracture near his right wrist. He hit .362 (17-for-47) in 12 games following his return.