The 26-year-old, who initially sustained the injury on April 11, was replaced on the roster by right-handed pitcher Scott Atchison from Triple-A Pawtucket.
Ellsbury had returned to competition on May 22 but began experiencing discomfort again in his left side and consulted with medical experts on Thursday and Friday.
"I tried to play with a level of discomfort, knowing that I wasn't 100 percent, and doing so worsened my condition," Ellsbury told the team's official website (boston.redsox.mlb.com).
"I saw a thoracic specialist today and he advised me I need to be at a further stage of healing before I resume play. I really don't have a timeline for when I'm going to come back."
Ellsbury is batting .250 with four doubles, three RBIs and seven runs in nine games for the Red Sox this season.
(Writing by Mark Lamport-Stokes in Los Angeles; Editing by Peter Rutherford)