The surgery will be performed by Dr. James Andrews, the team announced.
The Marlins said Capps is expected to require 10-12 months to recover, and they hope the right-hander will be ready for Opening Day in 2017.
Capps was expected to challenge incumbent A.J. Ramos for the closer's job. Last year, Capps had 58 strikeouts in 31 innings, and his rate of 16.8 strikeouts per nine innings was the highest in the majors among pitchers with at least 15 innings.
Information from The Associated Press was used in this report.