Yehonatan was born in Jerusalem in the Batei Ungarin neighborhood on 31 December 1928. His father was Tzvi, a rabbi, and his mother was Ahuva. He grew up in a haredi family of rabbis, with a half-dozen siblings. He studied in Talmud Torah and Yeshivat Hatam Sofer, and he received rabbinical ordination. He sought ways to break out of his haredi neighborhood, and private tutors and evening classes gave him the opportunity to receive a general education and even complete matriculation exams.