A powerful blast in the ancient city had raised fears the militant jihadists had escalated their push to rid Syria of what they view as un-Islamic artifacts after they destroyed the smaller Baal Shamin temple last week.
"We can confirm destruction of the main building of the Temple of Bel as well as a row of columns in its immediate vicinity," the UN training and research agency UNITAR said, providing satellite images from before and after the explosion on Sunday.
The 2,000-year-old Temple of Bel was the centrepiece of Palmyra's famed ruins and one of the most important relics of the heritage site, which has been described by the UN's cultural arm UNESCO as of "outstanding universal value".
Daesh fighters seized the city from Syrian regime forces in May and have since attacked the city's ruins and historic sites, which they consider idolatrous, and in mid-August beheaded the 82-year-old former antiquities chief in Palmyra.
The Sunni Muslim group has also been accused of destroying heritage sites to loot items to sell on the black market and to gain publicity for their campaign to bring vast swathes of Iraq and Syria under their own harsh interpretation of Islam.
The Syrian Observatory for Human Rights, a Britain-based monitor, said late Sunday that Daesh fighters had set off boxes and barrels of explosives inside the 2,000-year-old temple, destroying the inner part of the building.
"This was the most important temple for tourists and for the people of Palmyra. They used to hold festivals there," said Mohammad Hassan al-Homsi, an activist from Palmyra.
- 'Incalculable value ' -
UNITAR said its satellite programme put to rest any doubts that the Temple of Bel -- built between 32 BC and the 2nd Century, and which later served as both a church and a mosque -- had been destroyed in the blast.
A shot taken on August 27 clearly shows an erect, rectangular structure surrounded by columns, while a shot taken on Monday showed there was little left besides a few columns in the very outer edges of the site.
UN spokesman Stephane Dujarric said: "We condemn in the strongest possible terms the wanton destruction of a site of incalculable value to our shared global heritage."
UNITAR on Friday also presented satellite images confirming the destruction of the Baal Shamin temple, which the UN's cultural agency UNESCO called a "war crime". IS had previously released photographs purporting to show the destruction.
Syria's antiquities chief Maamoun Abdulkarim said the Temple of Bel was Palmyra's most important site.
"It is the best example of the combination of Oriental and Greco-Roman art styles," he said.
"Along with the temple of Baalbek in Lebanon, it is the most important temple in the Middle East... if its destruction is confirmed, it would be a huge loss not only for Syria, but for all the world."
France on Sunday condemned the attack "against a UNESCO-recognised archeological jewel" as evidence that Daesh "is persisting in its criminal determination to wipe out the cultural diversity in the Middle East".
Known as the "Pearl of the Desert", Palmyra, which means City of Palms, lies 210 kilometres (130 miles) northeast of Damascus. Before the Syrian conflict erupted 2011, more than 150,000 tourists visited the ruins every year.
Before the arrival of Christianity in the second century, Palmyra worshipped the Semitic god Bel, along with the sun god Yarhibol and lunar god Aglibol.
Daesh reportedly mined the ancient site in June before destroying the Lion Statue of Athena outside the Palmyra museum.
Most of the pieces in the city's museum were evacuated by antiquities staff before IS arrived, though the jihadists have blown up several historic Muslim graves.
Daesh has also executed hundreds of people in Palmyra and its surroundings, including several dozen soldiers in the city's ancient amphitheatre.
More than 240,000 people have died in Syria's conflict since it began with anti-government protests in March 2011.