The airliner, with 95 people on board, was seized on Tuesday after leaving Sudan's war-torn Darfur region for Khartoum. It was forced to land at the remote Sahara desert oasis of Kufrah in southeastern Libya.
The identity of the two hijackers and their motive for seizing the Boeing 737/200 was unclear.
The hijackers first released the passengers and two crew members, but kept six crew hostage while negotiations continued.
"The two hijackers were transported to one of the halls at Kufrah airport after giving themselves up," Libyan state news agency Jana quoted aviation authority head Mohamed Shlibek as saying.
Sudan's Civil Aviation Authority said Libyan authorities had arrested two Sudanese men, but it was not known why they seized the plane.
"That is now under investigation. All they have said is that they wanted to claim refugee status in Paris," Abdel Hafiz Abdel Rahim said.
The pilot told Libyan officials earlier that the hijackers were from a branch of the Sudanese Liberation Movement (SLM), a Darfur rebel group.
He said they wanted the plane to be refuelled so they could fly on to meet their leader Abdel Wahed Mohammed al-Nur in the French capital, Jana reported.
Rebel Link Denied
But Nur's faction strongly denied the hijackers were its members.
Another SLM faction that signed a 2006 deal with Khartoum, which was rejected by Nur, said the passengers on the hijacked plane had included seven of its officers, three of them members of a transitional Darfur regional government.
"Last night we felt terrorized," Mohamed al-Tijani Tayeb, one of the SLM transitional government members, told Libyan state TV, expressing relief at being free.
"We thank the Libyan authorities for this, the result of their peaceful dialogue."
Darfur has been riven by conflict since a rebellion against Khartoum's rule broke out more than five years ago. International experts say more than 2.5 million Darfuris have been driven from their homes and 200,000 people killed. Sudan puts the death toll at about 10,000.
The insurgents are split into numerous factions.
The plane had taken off from the South Darfur capital, Nyala, bound for Khartoum. Libya granted permission for the plane to land after the pilot said it was running out of fuel, Libya's state news agency said.
All the passengers were Sudanese except two Egyptian police officers, two Ethiopians and one Ugandan.
Libyan TV said the authorities gave medical treatment to some of the freed passengers who fainted in the plane after its air conditioning stopped working.
Another plane would take them on to Sudan on Wednesday, said aviation authority head Shlibek.
