Juan Lagares has been put on the disabled list and will have surgery to repair the partially torn ligament in his left thumb, Terry Collins told reporters.
According to Collins, Lagares will miss at least six weeks.
Lagares missed several games in June with the same condition, which he initially suffered making a diving catch on June 1.
Sandy Alderson and Terry Collins later said Lagares may eventually need surgery, but they hoped he would be able to wait until the offseason.
Brandon Nimmo was promoted from Triple-A to replace Lagares on the roster.
Nimmo, 23, hit .235 with one home run and four RBI in 16 games with the Mets before being demoted in mid July, when Michael Conforto returned from Triple-A.
MLB.com ranked Nimmo the organization's top prospect entering 2016, but dropped him to fifth in the system during their most recent update.