The procedure will be done on Monday in New York.
Andujar recently came off the injured list after missing most of April with the same ailment. He opted to avoid surgery when the tear was first discovered after playing his third game of the season. The 24-year-old only lasted nine contests before landing on the IL again.
The 2018 AL Rookie of the Year runner-up slashed .088/.114/.088 as the Yankees primary DH in his short-lived return.
Andujar's teammate, Gleyber Torres, had some sage advice for him following the team's doubleheader against the Baltimore Orioles.
"It's not that easy to have surgery and watch the game outside the field. I know how that feels," Torres said, according to Bryan Hoch of MLB.com. "I think it's the best option for him. ... It's not easy, but it's part of the life. Just be ready for the next season."
The Yankees have been decimated with injuries in 2019. The likes of Giancarlo Stanton, Aaron Judge, Luis Severino, and Didi Gregorius have all been shelved for a significant amount of time but are expected to return at some point this season.
Despite all the health issues, New York (26-16) is just a half game behind the Tampa Bay Rays for first in the AL East.