Unknown assailants gunned down Barghathi outside his home, Colonel Abdullah al-Zaidi, spokesman for the security services, told AFP.
He said Barghathi -- a former rebel leader in the 2011 uprising that toppled longtime dictator Moamer Kadhafi -- died of head and chest wounds at the Mediterranean city's Al-Jala hospital.
Barghathi was the first officer in Kadhafi's army to defect and form a rebel force in the revolt, Zaidi said.
Later today, members of the slain officer's Braghtha tribe fired rocket-propelled grenades at the home of another prominent former rebel they believed was behind the killing, according to a security source. The home was empty at the time.
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The group's headquarters were attacked in June by protesters seeking to drive militias out of the eastern city, sparking clashes in which more than 30 people were killed.
Benghazi was the cradle of the uprising that toppled Kadhafi's regime, but has since seen a series of assassinations targeting officers in the security services.
Other attacks have targeted Western interests and diplomats, and much of the violence -- including the killing of US ambassador Chris Stevens and three other Americans in an attack on the US mission last year -- has been attributed to radical Islamists.
Two years after the revolution, Libya's new authorities have failed to establish a new army and police force, and are still struggling to rein in tribal militias and groups of former rebels.