Palestinian spokeswoman Hanan Ashrawi said the vote was an affirmation of Palestinian sovereignty over the site that marks the place where Christians believe Jesus was born.
Israel angrily denounced the vote, with Foreign Ministry spokeswoman Ilana Stein saying the decision "has turned UNESCO into a theater of the absurd."
"This is a sad day for the World Heritage Committee," she said.
The 21-member committee, meeting in St. Petersburg, Russia, voted 13-6 to include the church and pilgrimage route, located in the Israeli-controlled West Bank, on its list of sites. There were two abstentions.
The drive to get the Nativity church quickly recognized as a World Heritage site was part of the Palestinians' bid to win international recognition since attempts to establish a Palestinian state through negotiations with Israel are frozen.
The United States was among nations opposed to the Palestinian proposal of an emergency candidacy for the iconic Christian site, shortcutting what is usually an 18-month-long process to apply for World Heritage recognition. Neither the United States nor Israel was on the committee. The U.S. ambassador to UNESCO, David Killion, said the United States is "profoundly disappointed."
The church — which drew some 2 million visitors last year and parts of which are 1,500 years old — stands above the grotto that Christians believe was the birthplace of Jesus. The Palestinian application asks for recognition as a site of "outstanding universal value" urgently in need of attention.
The application cited lack of regular restoration of the church due to the political situation since 1967 when Israel occupied the territories, and difficulties procuring equipment because of lack of free movement imposed by Israeli forces.
The United Nations Educational, Scientific and Cultural Organization voted to admit Palestine as a full member in October. The emergency candidacy for the church clearly showed the Palestinians' intention of making the most of their position, after a failure to join the main U.N. body because Palestine is not a recognized state.
The Palestinian application to place the Church on the list showed that they plan to put forward other sites for prestigious World Heritage recognition, eventually linking various landmarks to the life of Jesus.
"The message to Israel today is that unilateral actions will not work and that Israel cannot continue challenging the world despite its powerful allies," Ashrawi said.
Killion, the U.S. ambassador, said "this body should not be politicized." His statement noted the candidacy was opposed by a UNESCO experts committee, whose conclusions are almost always heeded.
The three churches acting as custodians of the site had also been opposed. The Greek Orthodox, Armenian and Roman Catholic churches keep the site under a so-called Status Quo agreement dating to the Ottoman empire, and fear the Palestinian action will upset that delicate balance.
"The site clearly has tremendous religious and historical significance," Killion's statement said. "However, the emergency procedure used in this instance is reserved only for extreme cases."
Stein, the Israeli Foreign Ministry spokeswoman, said those who voted in favor of the Nativity candidacy "have given themselves up as pawns in the service of the Palestinians at the expense of UNESCO's professionalism and good name."
While the church needs restoration, including repair of a leaky roof, it was not seen by the experts committee as being in imminent threat of destruction — the criteria usually reserved for the emergency procedure.
A site nominated by Israel depicting human evolution at Mount Carmel, the Nahal Me'arot/Wadi el-Mughara Caves, also was inscribed on the World Heritage list. That nomination, like all others under consideration in St. Petersburg, went through regular channels — not the emergency route.