Niese, who was examined at the Hospital for Special Surgery in New York, was scheduled to have surgery Thursday and is expected to be ready for Spring Training next year.
He was placed on the 60-day disabled list on Thursday and was replaced by veteran right-hander Elmer Dessens, whose contract was purchased from Triple-A Buffalo.
Niese left Wednesday's 9-0 win over the Cardinals at Citi Field in the top of the second inning after stretching to receive a throw while covering first base on a potential 3-6-1 double play. He went into a split, missed the bag and collapsed moments later while trying to throw a practice pitch with manager Jerry Manuel and the team training staff on the mound. The left-hander, who was 1-1 with a 4.21 ERA in five starts this season, was helped off the mound and into the clubhouse.
Niese is the fourth Mets starting pitcher to suffer an injury this season, joining Fernando Nieve, John Maine and Oliver Perez. Perez missed roughly two months with patellar tendinitis in his right knee before rejoining the rotation in July. Maine has not pitched since the first week of June because of weakness in his right shoulder.
Doug Miller is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.