The final version of the draft resolution was changed at the last minute to remove a controversial clause saying the Western Wall in Jerusalem, the holiest site at which Jews can pray, is an "integral part" of the Al-Aqsa mosque compound.
Israel had denounced the statement as "a clear endeavour to distort history" and appropriate the site.
The flashpoint compound, which is considered sacred to both Islam and Judaism, is located in the southeastern corner of the Old City in Israeli-occupied east Jerusalem. Muslims call it Al-Haram al-Sharif (the Noble Sanctuary) while Jews rever it as the Temple Mount which housed the First and Second Temples.
The resolution approved today -- which was drafted by Algeria, Egypt, Kuwait, Morocco, Tunisia and the United Arab Emirates -- condemns Israeli actions at the compound, including restricting access to Muslim worshippers during Eid celebrations last month on security grounds.
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It was supported by 26 of the 58 member countries on UNESCO's executive board, while 25 members abstained.
It was opposed by six countries: the United States, Britain, Germany, the Netherlands, the Czech Republic and Estonia.
It also calls for the "prompt reconstruction of schools, universities, cultural heritage sites, cultural institutions, media centres and places of worship that have been destroyed or damaged by the consecutive Israeli wars on Gaza.