The UNESCO resolution on "occupied Palestine" was endorsed Tuesday by the agency's executive board at its headquarters in Paris, after being approved at the committee stage last week.
Referring throughout to "the occupying power," it condemns Israel for restricting Muslims' access to the Al-Aqsa mosque compound -- Islam's third holiest site -- and criticises damage by security forces to the site and nearby excavations.
It is the latest episode in a series of rows at UNESCO, which is responsible for protecting important heritage sites and is one of few international organisations that recognises Palestine as a member state.
Israel suspended its cooperation with UNESCO last week in response to the draft resolution and its ambassador, Carmel Shama Hacohen, accused the Palestinians of playing "games" on Tuesday.
"This is the wrong place to solve problems between countries or people," he told AFP.
Israel is furious that the resolution refers to the Old City site in Jerusalem by its Muslim name, Al-Aqsa or Al-Haram al-Sharif.
It is considered holy by Muslims, Christians and Jews. Jews refer to it as the Temple Mount and it is considered the holiest site in Judaism.
Israeli Prime Minister Benjamin Netanyahu complained last week that saying "Israel has no connection to the Temple Mount and Western Wall is like saying China has no connection to the Great Wall of China or Egypt has no connection to the pyramids".
While acknowledging the importance of the Old City to "the three monotheistic religions" -- Islam, Judaism and Christianity -- the resolution focuses on Israeli restrictions on Muslims accessing the mosque.
It also includes condemnation of Israel's blockade of Gaza and "constant aggressions by the Israeli settlers" in the West Bank.
- Violations -
Deputy Palestinian ambassador to UNESCO, Mounir Anastas, welcomed the decision on Tuesday.
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"This resolution reminds Israel that they are the occupying power in east Jerusalem, and it asks them to stop all their violations, especially in the fields of competence of UNESCO such as the excavations," he told reporters.
Since 2011 when Palestine was admitted to UNESCO, the body has been the scene of numerous diplomatic spats resulting from resolutions condemning Israel, most recently in April but also in October last year.
The east Jerusalem site is a 14-hectare (35-acre) rectangular esplanade at the southeast corner of the Old City which was seized by Israel during the 1967 Six-Day War and later annexed in a move never internationally recognised.
Israel considers all of Jerusalem as its undivided capital, but the Palestinians want the eastern sector as capital of their future state.
- Unease in UNESCO -
The atmosphere before the vote on Tuesday was soured further by threats received by telephone and on social media last week following a vote on the draft resolution, a UNESCO official said.
The text had created unease at the top of the organisation, with Michael Worbs, who chairs UNESCO's executive board, saying he would have liked more time to work out a compromise.
The resolution was voted on last Thursday at the committee stage, with 24 votes in favour, six against and 26 abstentions. There were two absentees.
UNESCO chief Irina Bokova also distanced herself from the resolutions, saying in a statement that "nowhere more than in Jerusalem do Jewish, Christian and Muslim heritage and traditions share space."
Israel's envoy to UNESCO defended the Jewish state's suspension of its cooperation with the organisation as a "proportional reaction" to the resolution passed on Tuesday.
"I hope it will not last long," Shama Hacohen told AFP.
He also saw Mexico's decision to change its position Tuesday from voting in favour of the resolution to abstaining as a small victory.
"We hope it will come to a point that the Palestinians understand that there is no place for these games at UNESCO," he said.
The UN body also on Tuesday adopted a separate, less controversial resolution on schools in Palestinian territories.