The aircraft had been on an internal flight in Libya when it was diverted to Malta, 500 km north of the Libyan coast, after a hijacker told crew he had a hand grenade.
Maltese Prime Minister Joseph Muscat on Friday said the hijackers of a Libyan plane had "surrendered, searched and been taken into custody."
All hostages were released unharmed.
The Airbus A320 with 118 people on board was on an internal flight in Libya when it was hijacked and diverted to Malta where it landed before midday on Friday.
"According to radar information the plane was going to Malta, then it flew back as far as Tripoli airspace, then it turned back towards Malta again," said Farouk al-Wifati, head of Afriqiyah Airways office in Tripoli's Mitiga Airport
Authorities in Malta said the two hijackers had threatened to blow the plane up with a hand grenade.
An official from Afriqiyah Airways said the hijackers had earlier expressed a willingness to release all the passengers, but said they will keep the pilot hostage.
A Libyan television channel reported it had spoken by phone with a hijacker who described himself as head of a pro-Gaddafi party. Gaddafi was killed in an uprising in 2011, and Libya has been racked by factional violence since.
Muscat said the country's security forces and emergency operations were at the scene.
The plane landed in Malta at around 11:32 am. It is one of three A320s that Afriqiyah owns.