Rabbi Yaakov ben Aharon Sasportas was born in 5370 (1610) in Oran, Algeria, then under Spanish rule, into a distinguished family of scholars expelled from Spain that traced its descent, according to tradition, to the Ramban. A child prodigy, he joined the rabbinical court of Tlemcen at eighteen and became rabbi of the city at twenty-four; he later held the same office in other North African communities, including Salé.

Around 5406 (1646) he was imprisoned, and he afterwards left North Africa for Amsterdam, settling there in the early 1650s. In 1652 he published Toledot Yaakov, an index of biblical verses cited in the Jerusalem Talmud. He accompanied Rabbi Menasseh ben Israel to London to seek permission for Jews to settle in England, and was sent by the King of Morocco on a diplomatic mission to the Spanish court. In 5424 (1664) he became rabbi of the Portuguese community of London, but the outbreak of plague drove him to Hamburg, where he then served. He was also dayan and rosh yeshiva in Livorno.

When the messianic movement of Shabbetai Tzvi swept the Jewish world in 1665-1666, he was among the first and fiercest opponents of the false messiah, working through his letters to turn the public away from what he considered a delusion. He documented this struggle in Tzitzat Novel Tzvi, completed in Hamburg in 5433 (1673); an abridgment prepared by Rabbi Yaakov Emden appeared in 5497 (1737) together with his responsa, Ohel Yaakov, edited by his son Avraham.

Returning to Amsterdam, he headed the Etz Chaim yeshiva and, after the death of Rabbi Isaac Aboab da Fonseca in 1693, became rabbi of the Sephardic community, a post he held for the rest of his life. He passed away in Amsterdam on 4 Iyar 5458 (April 15, 1698), aged eighty-eight, and was buried in the Portuguese cemetery Beth Haim in Ouderkerk near Amsterdam, where his tombstone has survived intact.