Acting Prime Minister Mahmoud Jibril said he had been shot in the head in an exchange between Gaddafi loyalists and National Transitional Council fighters.
He confirmed that Col Gaddafi, who had been taken alive, had died before reaching hospital.
Nato's governing body, meeting in the coming hours, is expected to declare an end to its Libyan bombing campaign.
Nato Secretary-General Anders Fogh Rasmussen said that with the death of Col Gaddafi "that moment has now moved much closer".
"After 42 years, Col Gaddafi's rule of fear has finally come to an end," he said. "I call on all Libyans to put aside their differences and work together to build a brighter future."
Wild scenes of celebration continued late into the night in towns and cities across Libya at news of the colonel's death.
Groups of young men fired guns in the air, and drivers honked their horns in celebration.
In the capital, Tripoli, cars clogged the city centre.
Golden gun
Mr Jibril, number two in the National Transitional Council (NTC), held a news conference in Tripoli to confirm the colonel's death.
"We have been waiting for this moment for a long time. Muammar Gaddafi has been killed," he said.
Video footage suggests Col Gaddafi was dragged through the streets.
It is unclear from the footage, broadcast by al-Jazeera TV, whether he was alive or dead at the time.
Later, Mr Jibril told journalists that a "forensic report" had concluded that the colonel had died from bullet wounds after he had been captured and driven away.
"When the car was moving it was caught in crossfire between the revolutionaries and Gaddafi forces in which he was hit by a bullet in the head," he said, quoting from the report.
"The forensic doctor could not tell if it came from the revolutionaries or from Gaddafi's forces."
Earlier, some NTC fighters gave a different account of the colonel's death, saying he had been shot by his captors when he tried to escape.
One NTC fighter told the BBC that he found Col Gaddafi hiding in a hole, and the former leader had begged him not to shoot.
The fighter showed reporters a golden pistol he said he had taken from Col Gaddafi.
Arabic TV channels showed images of troops surrounding two large drainage pipes where the reporters said Col Gaddafi was found.
US President Barack Obama said it was a "momentous day" for Libya.
He said the country had a "long and winding road towards full democracy", but the US and other countries would stand behind Tripoli.
Col Gaddafi was toppled from power in August after 42 years in charge of the country.
He was making his last stand in Sirte alongside two of his sons, Mutassim and Saif al-Islam, according to reports.
Nato air strike
A body that officials identified as that of Mutassim has been shown on Libyan TV.
A reporter with Reuters news agency described how the body of Mutassim - the former national security adviser - had been laid out on blankets on the floor of a house in the city of Misrata, while people jostled to take pictures of the corpse with their mobile phones.
The body of Col Gaddafi was also taken to Misrata.
There are conflicting reports as to the whereabouts of Saif al-Islam.
Acting Justice Minister Mohammad al-Alagi told AP news agency that Saif al-Islam had been captured and taken to hospital with a leg wound.
But another NTC official said his whereabouts were unknown.
Nato, which has been running a bombing campaign in Libya for months, said it had carried out an air strike earlier on Thursday.
French Defence Minister Gerard Longuet said French jets had fired warning shots to halt a convoy carrying Col Gaddafi as it tried to flee Sirte.
He said Libyan fighters had then descended and taken the colonel.
Proof of Col Gaddafi's fate came in grainy pieces of video, first circulated among fighters, and then broadcast by international news channels.
The first images showed a bloodied figure presumed to be Col Gaddafi.
Later, video emerged of the colonel being bundled on to the back of a pick-up truck after being captured alive.
None of the video footage has been independently verified.
'Full of challenges'
Col Gaddafi's death came after weeks of fierce fighting for Sirte, one of the last remaining pockets of resistance.
A senior official, Mahmoud Shammam, told the BBC that fighting throughout Libya was over.
World leaders urged the NTC to carry through its promise to reform the country.
UK Prime Minister David Cameron, who had taken a leading role in Nato's intervention, said it was "a day to remember all of Col Gaddafi's victims".
UN Secretary General Ban Ki-moon called it a "historic" moment, but warned: "The road ahead for Libya and its people will be difficult and full of challenges."
China said the death of Col Gaddafi marked the turning of a page in Libya's history. It called for an inclusive political transition in Libya as soon as possible, to protect the unity of the country and restore social stability.
Russia's President Dimitry Medvedev said he hoped Libya could achieve a peaceful transition to a modern democratic state.
Officials said the NTC intended to announce the "liberation of the country" in the coming days, allowing them to begin pushing through democratic reforms that will lead to elections.
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