The official, who spoke on condition of anonymity, declined to reveal the name of the dead commando but US media -- as well as the Republican presidential candidate Mitt Romney -- identified him as 42-year-old Glen Doherty.
The former member of the famed special operations forces unit had been working on a mission to track down shoulder-launched surface-to-air missiles in Libya, according to ABC News.
US military and intelligence officials have warned that thousands of the weapons, so-called MANPADs, were unaccounted for after Libya's former dictator, Moamer Kadhafi, fell from power.
The former SEAL described his job in an interview with ABC last month, saying he had traveled across the country chasing leads and then once the weapons were found, his team would destroy them on the spot, the American television network said.
Tuesday's harrowing assault in Benghazi by heavily-armed militants also claimed the life of the ambassador to Libya, Chris Stevens, and a State Department information management officer, Sean Smith, US officials said on Wednesday.
A fourth victim has not been identified but Fox News reported he also was a former Navy SEAL working as a security contractor.
Doherty reportedly trained as a sniper and medical officer in a seven-year career with the SEALs, before leaving to work at a private security company.
According to an account of the attack from senior officials, Doherty was one of two people who died after staff were evacuated to an annex near the main US consulate building.
With the main building engulfed in flames, the annex then came under sustained gunfire until Libya forces eventually managed to restore order in the early morning hours.
At least three other Americans were wounded in the attack.
Although the Pentagon and State Department had yet to officially release Doherty's name or military background, presidential hopeful Mitt Romney issued a statement Thursday mourning the death of the ex-Navy SEAL, who was from Massachusetts, where Romney served as governor.
"Ann and I extend our deepest condolences to the family and friends of Glen Doherty, a native of Winchester, Massachusetts, who was among those killed in Tuesday's assault on our consulate in Libya," his statement said.
"Glen served America with bravery and distinction, and gave his life in an effort to save others."
The US State Department Thursday defended its security arrangements at the Benghazi consulate, even though dozens of militants were able breach the compound and keep US security teams at bay for hours.