In a statement, the Met said the investigation found that Levine, 74, abused "vulnerable artists in the early stages of their careers", adding that it would be impossible for him to continue his working relationship.
Levine officially retired as music director in April 2016, but had stayed on as music director emeritus and artistic director of the Met's young artist program.
The Met says claims its management or board had covered up information of Levine's conduct were unsubstantiated.
The Met did not release specifics of the evidence, though said that more than 70 people had been interviewed.
Mr Levine has led more than 2,500 performances at the Met, one of the world's most illustrious opera houses, and is often named among America's top conductors.
The alleged victim told Lake Forest police the sexual abuse started in 1985 when he was 15-years-old and Levine was in his early 40's.
Levine was held in very high esteem by the Met's orchestra, and was also music director of the Chicago Symphony Orchestra's Ravinia Music Festival from 1973-1993 and the Boston Symphony Orchestra from 2004-2011, and chief conductor of the Munich Philharmonic from 1999-2004.
After taking an nearly two-year health-related hiatus from conducting from 2011 to 2013, Levine retired as the Met's full-time Music Director following the 2015-16 season to become Music Director Emeritus. Levine denied the allegations of sexual misconduct, saying he wants to resume his work "with full concentration and inspiration".
Ashok Pai said he had been abused by Levine for years, beginning in 1986 near the Ravinia Festival in IL, when he was 16. The man said Levine would lay naked with him and touched his penis.