Fighting flared up again on Saturday when gunmen took control of a military base near Sebha, after several days of relative quiet, the government said.
But in the evening, defence ministry spokesman Abderrazak al-Shebahi said the army had recaptured the Tamenhant base.
He said the army was tracking the attackers after they fled into the desert.
Government warplanes also launched raids “against certain targets”, he added.
The spokesman also said the group was made up of supporters of dictator Moamer Kadhafi, who was ousted and killed by NATO-backed rebels in October 2011.
“We know them and we are going to track where they are going,” he said.