The Afriqiyah Airways Airbus A320 with 118 people on board was hijacked after taking off from Sabha, bound for the Libyan capital Tripoli.
Instead, the plane was diverted to Malta International Airport.
It appears the two hijackers are supporters of Libya’s late deposed leader, Muammar Gaddafi.
Images of the two men kneeling on the tarmac with their hands up appear to show the moment they were arrested by the Maltese authorities.
All the passengers – including one infant – and a number of the crew had already been released.
Malta’s PM 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.
Joseph Muscat said neither of the men, believed to be of Libyan nationality, had made any demands.
The prime minister told a press conference: “The two hijackers have been detained in custody and interrogations are ongoing. The rest of the crew and passengers are also being questioned to ascertain events.
“Once this interrogation process is completed over the next few hours arrangements will be made to send the passengers and the crew members back to Libya with another Afriqiyah aircraft.”
Shortly before the incident drew to an end, one man emerged from the plane briefly and stood on the plane steps waving a green, Gaddafi-era flag – adding support to earlier suggestions they were loyalists to the former leader, killed in 2011.
Taher Siala, the foreign minister of Libya’s internationally backed Government of National Accord, said the hijackers wanted to set up a pro-Gaddafi political party.
One of the hijackers told a Libyan TV station: “We took this measure to declare and promote our new party.”
The incident began after the plane took off from Sabha at 11:10 local time, landing in Malta two hours and 20 minutes later.
PM Joseph Muscat said the passenger list included 82 men, 28 women and one baby.
Malta International Airport was closed and all flights were diverted while the incident was on-going.
Libya has been in a state of chaos since the 2011 overthrow of Muammar Gaddafi, who had ruled the country since 1969.
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