Hacham Hezekiah Shabtai was born to his mother Rachel, daughter of Perla, and to his father Hacham Gabriel Yehoshua Shabtai in 1862 in the city of Salonika, Greece. In 1867, at the age of 5, he immigrated to Israel with his parents and they settled in Jerusalem.
Hacham Hezekiah Shabtai studied in the Chessed El yeshiva in the Old City of Jerusalem and with his father, who was one of the yeshiva headmasters. In 1879 he married Hannah, the daughter of Rabbi Elazar Mizrachi, and they had several sons and daughters.
In 1886 Hacham Hezekiah Shabtai jointly authored Me'am Lo'ez, a commentary on the Book of Exodus, with Hacham Nachman Battito and HachamShmuel Nissim.
In 1889 he left as a rabbinic emissary for Tunis and Tripoli, and in 1890 he went to Buchara.
In 1900 he was appointed Associate Hacham Bashi in Jaffa and in 1904 appointed Hacham Bashi in Tripoli, Libya; in 1908 he was appointed Hacham Bashi in Aleppo, Syria, serving in this role for eighteen years.
While in his position, as a result of the Young Turks rebellion, he dealt with changes in the regime as well as with the imposition of the military draft on Jews. Hacham Hezekiah Shabtai stood his guard and defended the community. He took care of the release of three hundred scholars from hard labor and saved the Jewish cemetery from destruction.
In 1919 he left for London and Paris on a mission to raise funds for the establishment of an orphanage in Aram Tzuba (Iraq). In 1926, following a divergence in views with the heads of the community in Aleppo, he resigned from his position and returned to Jerusalem, where he was appointed Rosh Av Beit Din [Head of the Rabbinic court]. In 1940 he was chosen as a member of the Chief Rabbinic Council, and in 1943 he established the Sha'arei Ora yeshiva in Jerusalem.
Hacham Hezekiah Shabtai passed away on 23 Av 1955 and was buried in Jerusalem.
Hacham Hezekiah Shabtai's book, Divrei Hizkiahu, published in two volumes, contains sermons, responsa and halachic rulings.