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 during further negotiations before surrendering.
Released passengers who flew back to Khartoum late on Wednesday said that 10 minutes into the flight the two hijackers had stood up, brandishing handguns.
The plane had taken off from the South Darfur capital Nyala, bound for Khartoum. Libya granted permission for it 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.
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