The stone temple is a few hundred feet from Thailand's eastern border with Cambodia.
The temple is culturally Cambodian, sharing the Hindu-influenced style of the more famous Angkor Wat in northwestern Cambodia.
Honoured too by Unesco were two cities of the Straits of Malacca, Melaka and George Town, both in Malaysia, and the Kuk Early Agricultural Site in Papua New Guinea, marking the country's first entry on the list.
Cambodia started seeking the status for Preah Vihear in 2001, hoping for the influx of tourism and international funding that normally accompanies the designation.
In the past, Thailand has vetoed its neighbour's submissions amid fears the status would include disputed land along the border.
|The temple style shows Hindu influence
But in May, the government of Samak Sundaravej bypassed the parliament and endorsed Cambodia's application.
A month later Noppadon Pattama, the Thai foreign minister, signed a joint communique with Cambodia, endorsing the country's bid to nominate the temple as a world heritage site.
However, Thai critics accused him of violating the country's soveriegnty, and the government withdrew its support.
Thailand's cabinet suspended its decision to support Cambodia's bid on July 1.
Thailand's action had little effect on Preah Vihear's World Heritage application, since Cambodia does not need Thailand's support.
Hor Namhong, the Cambodian foreign minister, has accused Thai opposition politicians of exploiting the cross-border dispute to advance their own domestic political agenda and warned they might endanger bilateral relations.
For his part, Cambodia's prime minister, welcomed the Unesco decision in a statement on Tuesday.
"This is a new pride for the people of Cambodia," Hun Sen said.
But he reassured Thailand, saying that the temple's inscription "does not affect" the negotiations to resolve problems of border line between the two nations.