The soldiers were in their way from Al-Jufra to Misrata when gunmen believed to be affiliated with IS opened fire at the bus in Alload area, south of Sirte.
2 soldiers were killed and 3 others injured in an exchange of fire. 2 attackers were also killed.
In June, 5 soldiers from the Third Force were killed at a fake checkpoint in the same area and authorities in Misrata accused former regime followers of being behind their killing.
The Third Force was tasked in 2013 to protect the south.
Meanwhile, 5 Sabha-bound fuel tanker drivers from Misrata were abducted Tuesday by IS militants near Abu Garain town, 118 km south of Misrata. Reports say the drivers were later released and the 5 tankers were taken to Sirte.