The United Nations' cultural arm declared the Old City of Hebron a protected heritage site in a secret ballot, an issue that has triggered a new Israeli-Palestinian spat at the international body.
UNESCO voted 12 to three - with six abstentions - to give heritage status to Hebron in the Israeli-occupied West Bank.
Hebron is home to more than 200,000 Palestinians and a few hundred Israeli settlers, who live in a heavily fortified enclave near the site known to Muslims as the Ibrahimi Mosque and to Jews as the Tomb of the Patriarchs.
The resolution, brought by the Palestinians and which declares Hebron's Old City as an area of outstanding universal value, was fast-tracked on the basis that the site was under threat, with the Palestinians accusing Israel of an "alarming" number of violations, including vandalism and damage to properties.
On Tuesday in a separate vote, the heritage committee backed a resolution condemning Israeli actions in Jerusalem, sparking Israeli anger.
Israel says the Hebron resolution - which refers to the city as Islamic - denies thousands of years of Jewish connection there.
Hebron claims to be one of the oldest cities in the world, dating from the chalcolithic period or more than 3,000 years BC, the UNESCO resolution said.
The resolution is seen as a victory for Palestinian diplomacy and would be cited by Israel as a fresh example of what it alleges is the UN's inherent anti-Israel bias.
In May Israel reacted furiously after UNESCO passed a separate resolution on Jerusalem, and has recently prevented UNESCO researchers from visiting Hebron.
Source: News agencies