"Israel will not sit by while the organization calls for the denial of our sovereignty in Jerusalem", he added.
Tweeting on his official account following the decision, Minister of Foreign Affairs Ayman Safadi said Jordan highly valued such a decision.
Israel said Wednesday it would further reduce the amount it pays annually to the United Nations in retaliation for the latest resolution critical of its policies. "Grateful", the foreign minister tweeted. Israel considers Jerusalem its undivided capital but Palestinians seek east Jerusalem for the capital of a future state.
The resolution - which passed with 22 UNESCO member-states voting in favor, 10 voting against and 23 abstaining - also criticized Israel for carrying out what it described as "persistent excavations, tunneling, works and projects in East Jerusalem, particularly in and around Jerusalem's Old City".
The original draft sought to reaffirm 18 previous UNESCO resolutions against Israel on the matter of Jerusalem, including resolutions denying Israeli sovereignty over the city as well as any Jewish link to the Temple Mount and the Western Wall.
Israeli Minister of Culture and Sport Miri Regev is to call for the closing of the Jerusalem offices of UNESCO, the United Nation's cultural body, at a cabinet meeting on Wednesday in Jerusalem, Israel's Channel 2 reports.
It was then voted for by Russia, China, Brazil, Sweden, South Africa, Iran, Malaysia, Mauritius, Nigeria, Senegal, Bangladesh, Pakistan, Vietnam, Nicaragua, Chad and seven Arab countries.
The statement referenced negotiations held by the EU with the Palestinians and Jordanians to water down the text, and said that Sweden was willing to make concessions to other EU partners in order to reach a united EU position on the matters.
"Today there are more countries abstaining or supporting Israel than countries against Israel", Netanyahu said.
"We are working constantly to increase support for Israel in worldwide bodies in order to reflect our growing status vis-à-vis bilateral contacts with countries", Netanyahu said.
Netanyahu referred to the pro-Israel votes as "one point of light".