Capps has a torn ligament in his throwing elbow that requires Tommy John surgery, and the operation was to be performed Tuesday by specialist Dr. James Andrews in Gulf Breeze, Florida.
Capps is expected to return for opening day 2017.
"It’s definitely a loss," manager Don Mattingly said. "Carter, when he was in there, was as dominant as it gets last year."
Capps had 58 strikeouts in 31 innings last year, and his rate of 16.8 strikeouts per nine innings was the highest in the majors among pitchers with at least 15 innings. But he missed the final two months of the season because of elbow soreness, and sat out three months in 2014 for the same reason.
Miami had expected the right-hander to challenge incumbent A.J. Ramos for the closer's job. But last week Capps cut short a throwing session and underwent an MRI last week after his elbow again flared up.
The Marlins' team doctor determined Capps had torn his ulnar collateral ligament, and Andrews confirmed the diagnosis Monday. Marlins president of baseball operations Michael Hill declined to blame the injury on Capps' bizarre hop-skid-and-hurl motion.
"It's pitching," Hill said. "No matter what the delivery, it's a tough sport for pitching."
Right-hander Bryan Morris becomes the leading candidate for eighth-inning duty, with Kyle Barraclough also a contender. A trade for more bullpen help is a possibility.
"If there's an opportunity to upgrade, we'll do so," Hill said, "but we're happy with the arms we have in camp."