In an investigation published on its website and based on extensive reporting in the Libyan city, the Times yesterday said the killing of US ambassador Chris Stevens and three of his countrymen was the work of local fighters.
The report could likely stir up controversy in Washington, where the Obama administration has repeatedly been accused of covering up what happened in Benghazi - a charge it denies.
The newspaper also said the attack may indeed have been sparked by citizens who headed to the US mission after being angered by an anti-Islamic video that had aired on local television channels.
"The attack was led, instead by fighters who had benefited directly from NATO's extensive air power and logistics during the uprising," against the country's long-time dictator Moamer Kadhafi, killed in October 2011.
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The newspaper, citing American officials briefed on a criminal probe into the killings, alleged that a local rebel leader named Ahmed Abu Khattala, said to have disdain for the United States despite its help to overthrow Kadhafi, is the prime suspect for orchestrating the Benghazi killings.
"Mr Abu Khattala declared openly and often that he placed the United States not far behind Colonel Kadhafi on his list of infidel enemies," the newspaper said.
"But he had no known affiliations with terrorist groups, and he had escaped scrutiny from the 20-person CIA station in Benghazi that was set up to monitor the local situation," the report added.
The Times said Abu Khattala was "a central figure" in what unfolded, citing numerous Libyans present at the time, but also reported that the attack had "spontaneous elements."
But US officials later said that some of those behind the assault had links to organised Al-Qaeda extremists and that it was an act of terrorism.
The Times yesterday reported: "Anger at the video motivated the initial attack. Dozens of people joined in, some of them provoked by the video and others responding to fast-spreading false rumours that guards inside the American compound had shot Libyan protesters.