Libya’s interior minister, Wanis al-Sharif, confirmed J. Christopher Stevens and the officials died in an overnight attack on Tuesday.
The US State Department has also confirmed the death.
Stevens, a career officer with the US foreign service, only took up the post four months earlier and was visiting Benghazi at the time.
The envoy died, reportedly from suffocation, when an armed mob protesting against a film deemed offensive to Islam attacked the US mission.
Abdelmonoem al-Horr, a spokesman for the Libyan interior ministry’s security commission, said rocket-propelled grenades were fired at the consulate from a nearby farm.
Witnesses said the attackers ripped up a US flag then looted the consulate before setting it on fire on the 11th anniversary of the September 11 attacks in the United States.
Before confirmation of Steven’s death, US Secretary of State Hillary Clinton said: “we are heartbroken by this terrible loss” of a State Department official.
Just hours earlier, Islamists also stormed the US embassy in the Egyptian capital, Cairo.
The United States has since stepped up security at the Cairo consulate.
The US State Department Spokeswoman, Victoria Nyland, said protesters in Cairo ripped down the US flag and replaced it with a plain black flag during the protests.
A trailer of the film Innocence of Muslims by an Israeli-American was uploaded to Youtube and reportedly described Islam as a “cancer” and depicted the Prophet Mohammed sleeping with women.
Muslims regard depictions of the Prophet as offensive.
The movie was directed and produced by Sam Bacile, a 52-year old real-estate developer from southern California.
The film is being promoted by the controversial Florida pastor Terry Jones, who has drawn protests in the past for burning the Koran and vehemently opposing the construction of a Muslim cultural centre near Ground Zero in New York.