Gregorius underwent an MRI on Thursday. Gleyber Torres is likely to move over to shortstop in his absence.
Boone said he was confident Gregorius will play the majority of the 2019 season, even though the surgery often requires more than a year of rehabilitation and recovery when performed upon pitchers.
General manager Brian Cashman estimates a summer return for Gregorius.
Gregorius had two stints on the disabled list this season; one that lasted almost two weeks after he suffered a left heel contusion in late August and the second where he almost missed the entire postseason after he tore cartilage in his right wrist while sliding home. Gregorius was cleared to resume baseball activities on September 28 and returned to the Yankees' lineup.
Gregorius hit.268 with 27 home runs, 86 RBIs and an.829 OPS in 134 regular-season games this season.
The injury to Gregorius could lead to interest in free agent Manny Machado.