AntarZouabri had been blamed for the deaths of thousands of civilians since he took command of the radical Islamist group in 1996.
Zouabri's death has been reported by local newspapers before, but this is the first time it has been confirmed by the government.
Zouabri has led the Armed Islamic Group since the group's former leader, Djamel Zitouni was killed in 1996 as part of a settling of scores within the group.
The GIA killed the AIS leader for central Algeria, Azzedine Baa, in December, and in January pledged to fight the AIS as an enemy; particularly in the west, full-scale battles between them became common.
In July 1996, GIA leader Djamel Zitouni was killed by one of the breakaway factions - Ali Benhadjar's Medea brigade, later to become the AIS-aligned Islamic League for Preaching and Combat - and was succeeded by AntarZouabri.
Under the leadership of AntarZouabri, its longest serving "emir" (1996-2002), the GIA became a "takfirist" group, considering Algerian society to be in violation of Islamic precepts, therefore justifying the killing of members of that society as a form of purification of heretical elements.