"Israel completely rejects this preposterous resolution. Jerusalem is our capital, always was, always will be," Netanyahu said in an English-language video posted online by his spokesman.
"But I do appreciate the fact that a growing number of countries refuse to participate in this theatre of the absurd," said the Israeli leader.
"Especially I want to again express our thanks to President (Donald) Trump and Ambassador (Nikki) Haley for their stalwart defence of Israel and their stalwart defence of the truth."
But 35 countries abstained including Argentina, Australia, Canada, Croatia, the Czech Republic, Hungary, Latvia, Mexico, the Philippines, Romania and Rwanda.
Ukraine, which supported the draft resolution at the Security Council, was among 21 countries that did not turn up for the vote.
Trump had warned ahead of the vote in the 193-nation assembly that "we're watching" and threatened reprisals against countries backing the measure, which reaffirms that the status of Jerusalem must be resolved through negotiations.