Israel previously said it intended to leave the Paris-based agency, citing “systematic attacks on the Jewish state.”
Azoulay said in a statement on Friday she deeply regretted the withdrawal, which is set to take effect on Dec. 31 2018.
She added: “It is inside UNESCO and not outside it” that countries can overcome their differences.
Israel’s decision came on the heels of the United States announcing its withdraw from UNESCO over similar allegations of anti-Israel bias at the agency, where the Jewish state and its allies are far outnumbered by Arab countries and their supporters.
Many Israeli’s viewed recent resolutions by the organization as diminishing Jewish ties to Jerusalem and the biblical city of Hebron.