"We do believe the stress reaction is what has been bugging him all the way back to the end of May," team president Theo Epstein said on a conference call with reporters.
Epstein indicated Darvish also has a triceps strain but said it's the stress reaction that is knocking him out for the year.
"At least now we understand what he's been dealing with," Epstein said. "We had a pitcher last year, Alec Mills, who experienced the same thing. It took him a while to get diagnosed. Stress reactions are difficult to diagnose. They don't show up right away on normal scans."
Darvish left a rehab start after one inning on Sunday experiencing the same pain that has kept him out of the lineup most of the year. It was the second time he had a setback rehabbing this injury. He was shut down after a previous rehab outing as well.
"During warm-ups the next inning, I felt something in there,'' Darvish said Sunday. "Last time [in June] I did feel the same thing, [but] I continued to throw. This time I stopped."
Darvish started eight games for the Cubs in the first season of a six-year, $126 million contract he signed last offseason. He was 1-3 with a 4.95 ERA before going down in May.
"Really disappointed," Epstein said. "At least we have some clarity."
Epstein indicated it would be hard to find extra pitching at this time of year but also noted the Cubs have been playing without Darvish for most of the season. He also found one bright spot, as Darvish continues his post-Tommy John surgery career.
"I should note there was some good news with the testing," Epstein said. "His ligament that was reconstructed looked really good and in place and stable."
The Cubs are hopeful rest will be the answer to Darvish's current ailment, instead of going under the knife again, albeit for a different injury.
"If you let a stress reaction get too significant, and go without rest, it can often lead to a stress fracture which is more difficult to resolve," Epstein said. "The scans revealed no fracture."