Haftar's self-styled Libyan National Army seized Al-Jufra base 500 kilometres (300 miles) south of Tripoli, LNA spokesman Khalifa al-Abidi said.
The base had been occupied by the Benghazi Defence Brigades coalition, a rival to Haftar's forces that includes Islamists driven out of Libya's second city.
Abidi said the LNA also took the nearby towns of Houn and Soukna where they found ammunition depots and vehicles.
There was no immediate information about casualties.
Signup to our newsletter and follow us on Facebook and Twitter!
Haftar's forces now control all the major cities and military bases in the desert south of the North African country.
On May 25, they seized the Tamenhant base near Sebha after driving out a militia loyal to the internationally recognised administration, the Tripoli-based Government of National Accord (GNA).
The LNA had vowed to avenge an attack on its Brak al-Shati air base northeast of Tamenhant, in which 141 people including civilians were killed.
The GNA condemned that deadly assault, said it had not ordered it and announced an inquiry.
Libya has been wracked by chaos since the 2011 uprising that toppled and killed longtime dictator Moamer Kadhafi, with rival authorities and militias battling for control of the oil-rich country.