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".