U.S. special forces boarded the tanker a week ago off Cyprus, days after it left Es Sider port, which is controlled by rebels who demand more autonomy and oil wealth in defiance of the central government.
A Reuters reporter was allowed to board the Morning Glory moored near the Tripoli coast, witnessing how Libyan navy forces arrested the 21-strong crew and three rebels who had boarded the ship at Es Sider.
It was a rare victory for Tripoli, which is struggling to end a port blockade by rebels, one of many challenges facing the central government which has failed to secure the North African country three years after the fall of Muammar Gaddafi.
Former anti-Gaddafi rebels and militias refuse to surrender their weapons and often use force or control of oil facilities to make demands on a state whose army is still in training with Western governments.
Tired-looking Pakistani captain Mirza Noman Baig showed navy personnel the damage resulting from a fire fight with the Libyan navy before the vessel escaped from Libya. "This all," he said, referring to cracks and bullet holes on the tanker's crew office and an oil tank.
Libyan soldiers removed the crew on a small boat where they huddled in the open in the back on their way to Tripoli port.
"They will be referred to the relevant judicial authorities," said Lieutenant Colonel Salim ash-Shwirf, standing on the tanker. "The 21 and the Libyans are in good health but there are some damages at the tanker."
The crew declined to give interviews but the family of the captain say armed Libyan rebels boarded the ship, forced them to load crude and to evade the Libyan navy sent to stop them.
The Reuters reporter was shown two rifles, three pistols and bags full of ammunition in the crew's office. The rifles belonged to the three rebels, who had been handcuffed, a navy officer said.
The tanker carried no flag. The ship, which had been North Korean-flagged until Pyongyang denied knowledge of the vessel, was due to arrive later at Libya's Zawiya port, where its cargo of crude will be fed into the Zawiya refinery.
"The crew of the oil tanker is now under my authority and is being investigated," Libya's state prosecutor Abdelqadir Radwan told Reuters.
Eastern federalist leader Ibrahim Jathran, whose fighters seized three ports last summer, is demanding a greater share in Libya's oil resources and more autonomy for his region where many feel they have been abandoned by Tripoli for years.
The Tripoli government gave Jathran a two-week deadline on March 12 to end his port blockade or face a military assault, though analysts say Libya's nascent armed forces may struggle to follow through on the ultimatum.
Western governments, which backed NATO's air strikes to help the 2011 anti-Gaddafi revolt, are training Libya's armed forces and are pressing the factions to reach a political settlement.
But the powerful rival militias, with bases in the east and west of the country and political allies in the parliament, remain power brokers in a country where weapons from Gaddafi's era and the NATO-backed rebellion are easily available.
In another sign of chaos, an Italian construction worker was kidnapped near the eastern city of Tobruk. There has been no communication from his kidnappers as yet, the Italian Foreign Ministry on Sunday, adding he was a diabetic who did not have his insulin supplies with him.
Italy said Gianluca Salviato was snatched on Saturday by a gang it suspected of being a criminal organisation intending to seek a ransom, rather than an Islamist group.
(additional reporting by Ulf Laessing and Feras Bosalum; Writing by Patrick Markey and Ulf Laessing; editing by Sonya Hepinstall and Keiron Henderson)