Matz had been pitching with the elbow issue for much of the season and had intended to have the procedure performed this winter. However, he had not appeared in a game since Aug. 14 because of a left shoulder impingement that was irritating the rotator cuff.
With that discomfort persisting, Matz will be shut down and have the elbow procedure now. No surgery is planned for the shoulder issue.
The Mets have estimated a three-month recovery time for the elbow procedure, so Matz should be ready for spring training. The surgery will be next week at the Hospital for Special Surgery in Manhattan.
Matz, 25, went 9-8 with a 3.40 ERA in 22 starts during what was considered his rookie season, even though he also contributed with the Mets in 2015.
He becomes the latest starting pitcher to be shut down by the Mets for the remainder of 2016.
Matt Harvey underwent surgery in July to remove a rib and alleviate thoracic outlet syndrome. Jacob deGrom underwent surgery Wednesday to move the ulnar nerve in his pitching elbow. Zack Wheeler's intended return from Tommy John surgery has been tabled until next season because of multiple setbacks from the original March 2015 procedure.
As a result, the Mets will rely on a pair of rookies in the postseason rotation if they are able to qualify. In addition to Noah Syndergaard and Bartolo Colon, right-handers Seth Lugo and Robert Gsellman are expected to round out the Mets' starting pitching corps in October.
The Mets have acknowledged that Syndergaard also has a bone spur in his pitching elbow. However, team officials have indicated Syndergaard will not need to have the issue addressed by surgery this offseason.