"Final crew members leaving aircraft with hijackers," Maltese Prime Minister Joseph Muscat said on Twitter.
Minutes later, he added: "Hijackers surrendered, searched and taken in custody".
Libyan Foreign Minister Taher Siala said the two hijackers were supporters of slain dictator Moamer Kadhafi and had requested political asylum in Malta.
Siala, from Libya's internationally backed Government of National Accord, said the hijackers have also said they want to set up a pro-Kadhafi political party.
After more than an hour on the tarmac, the door of the Airbus A320 opened and a first group of women and children was seen descending a mobile staircase.
Dozens more passengers were released minutes later following negotiations that Maltese government sources said were led by the head of Malta's military.
In all, there were 111 passengers, including 28 women and a baby, on board, as well as seven crew members.
Maltese government sources had earlier said only a single hijacker was believed to be on the plane.
The aircraft had been on a domestic Libyan route operated by Afriqiyah Airways from Sabha in southern Libya to the capital Tripoli but was re-routed.
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