Israeli Prime Minister Benjamin Netanyahu praised the US decision as "brave and moral", a statement said.
The agency is known for designating world heritage sites such as Syria's Palmyra and the US Grand Canyon.
Unesco head Irina Bokova earlier called the US withdrawal a matter of "profound regret".
The US withdrawal will become effective at the end of December 2018 - until then, the US will remain a full member. The US will establish an observer mission at the Paris-based organisation to replace its representation, the state department said.
Israeli Prime Minister Netanyahu tweeted he had instructed his foreign ministry to "prepare Israel's withdrawal... in parallel with the United States".
Why does Trump dislike Unesco?
By Jonathan Marcus, BBC diplomatic correspondent
Unesco is an easy target for US President Donald Trump - it is a multilateral body with educational and developmental goals like promoting sex education, literacy and equality for women.
The US withdrawal will be seen by many as a manifestation of Mr Trump's "America First" approach and his across-the-board hostility to multilateral organisations; the irony being that Unesco is part of the international architecture that the US helped to establish in the wake of World War Two.
But it is the organisation's perceived anti-Israel bias that is the fundamental issue here. It has condemned Israel in the past for its activities in the West Bank and East Jerusalem, and earlier this year it designated the old city of Hebron a Palestinian World Heritage Site - a step Israel insisted denied centuries of Jewish history there, not least the Tomb of the Patriarchs that dates back to biblical times.