UNESCO is a specialized agency in the United Nations that encourages worldwide peace and security through education, science, culture and communication.
"This decision was not taken lightly, and reflects United States concerns with mounting arrears at UNESCO, the need for fundamental reform in the organization, and continuing anti-Israel bias at UNESCO", she added.
Nauert also clarified that, in accordance with the charter of UNESCO, the decision on "the USA withdrawal will enter into force on December 31, 2018".
The lack of staffing and funding plans for Unesco by the U.S. have been accompanied by repeated denunciations of Unesco by senior USA officials, including U.S. ambassador to the United Nations Nikki Haley.
UNESCO is best known for its work to preserve heritage, including maintaining a list of World Heritage sites, and programmes to promote education in developing countries.More news: 'Breaking Bad' house owners build fence to prevent trespassers
In October, Israel suspended its co-operation over a draft resolution referring to the Old City of Jerusalem as part of "the cultural heritage of Palestine".
The agency is in the process of choosing a new leader, with Qatari and French former ministers Hamad bin Abdulaziz al-Kawari and Audrey Azoulay neck-and-neck in the contest to replace Ms Bokova.
The Trump administration has been preparing for a likely withdrawal for months, and a decision was expected before the end of the year, according to USA officials.
The United States - one of the body's founding members - has withdrawn once before under president Ronald Reagan, who quit in 1984 over alleged financial mismanagement and anti-US bias in some of its policies.
Chris Hegadorn, the U.S. Charge d'Affaires and ranking U.S. representative to UNESCO, told The Associated Press on Thursday that the decision to pull out was linked to "the unfortunate politicization of the mandate of UNESCO, where anti-Israel bias has been a major factor and something the U.S. has been struggling to address".More news: Walmart Is Adding Super Fast Online Returns
Behind them in the secret ballot was an Egyptian career diplomat, Moushira Khattab, with 13 votes, and Tang Qian of China with five, according to results posted on Unesco's website. Permanent Representative to the UN Nikki Haley has repeatedly denounced these actions, and said the USA was "evaluating" whether or not it should continue as a member of the organization. It might be alluding to the fact that Palestine, which has not been granted full membership to the United Nations, is a UNESCO member, and that the West Bank city of Hebron was recently named an official world heritage site in a UNESCO statement that also called Israeli occupation of the territory illegal.
The United Nation's education, cultural and scientific agency has passed several resolutions against Israel.
"Among other efforts, UNESCO is committed to building the capacity of various individuals and stakeholders to develop and amplify innovative responses against extremism; all while promoting the protection of freedom of expression, privacy and other fundamental freedoms", Bokova wrote in a CNN op-ed in September.More news: Turkish troops prepare to enter Idlib province, Syria