Ellsbury initially suffered a hairline fracture of four ribs in a collision with team mate Adrian Beltre on April 11 and then sustained an additional injury on May 23 while making a diving catch against the Philadelphia Phillies.
The 26-year-old was put on the 15-day disabled list at the end of last month and will spend the next two weeks working on non-baseball activities at the Athletes Performance Institute in Arizona.
"Jacoby will require several weeks of rest and physical therapy," Red Sox medical director Dr. Tom Gill and Los Angeles-based Dr. Lewis Yocum said in a joint statement.
"This fracture, which is in a different area than the initial fractures and which was not present on previous scans, is likely the result of a new injury which occurred when Jacoby dove and impacted the ground during his brief return to play."
Ellsbury played only three games for the Red Sox in six weeks before returning to competition on May 22. He then experienced further discomfort in his left side before consulting with medical experts.
The American League's stolen base leader in 2008 and 2009, 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 Frank Pingue)