Cubs manager Jim Hendry said the MRI confirmed the diagnosis by team orthopedic specialist Stephen Gryzlo, who did a physical exam of the right-hander on Wednesday.
Zambrano received anti-inflammatory medication and will be sidelined for a few days. Hendry said the right-hander should resume throwing next week when the Cubs are in St. Louis.
"We look at hopefully getting him a start the last day of the trip in Houston," Hendry said.
Zambrano had taken himself out of his start Tuesday against Houston after five innings because he was feeling discomfort in his shoulder. In that game, he threw 86 pitches over five innings. Zambrano was placed on the disabled list in June because of discomfort in his right shoulder. He is 13-5 with a 3.58 ERA in 27 starts this year.
Zambrano's next scheduled start was to be Sunday in Cincinnati, but left-hander Sean Marshall will take Zambrano's place.
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.