The Afriqiyah Airways Airbus A320 flight with 118 people on board was hijacked after taking off from Sabha, bound for the Libyan capital Tripoli and was diverted to Malta International Airport instead.
It appears the two hijackers are supporters of Libya's late deposed leader, Muammar Gaddafi.
All the passengers - including one infant - and a number of the crew had already been released.
Maltese Prime Minister Joseph Muscat initially said that the men had been armed with pistols and a grenade - but later tweeted that the weapons appeared to be replicas.
Mr Muscat said neither of the men, believed to be of Libyan nationality, had made any demands and that interrogations are underway.