Benvenisti was born in 1934 in Jerusalem, his father was David Benvenisti, a Greek Jew originally from Thessaloniki and recipient of the Israel Prize, while his mother Leah (née Friedman) was Lithuanian Jewish. He was the brother of Refael (Rafi) Benvenisti, and father of Eyal Benvenisti. He graduated from the Leyada and served his compulsory military service in a Nahal unit near the Israeli–Lebanese border at Kibbutz Gesher HaZiv. In the early 1950s, following his discharge, he moved to the nearby Kibbutz Rosh Hanikra and served as a youth movement leader. He enrolled at the Hebrew University after his return to Jerusalem in 1955, studying both economics and medieval history. He later published books and maps on the period of the Crusaders in the Holy Land. During his years as a student, he headed the Hebrew University student union and the National Union of Israeli Students. He later obtained a doctorate from Harvard University's Kennedy School for his work on conflict management in Jerusalem and in Belfast.