Al-Kharafi group sought to have the opulently-furnished Airbus A340 seized over a debt related to a contract to build a beach resort in Libya.
Reviled by Libya's rebels as a symbol of Kadhafi's extravagance, the four-engined jetliner boasts a double bed, silver leather sofas, a private cinema and first-class seating for the dictator's female bodyguards and other staff.
In 2012, shortly after Kadhafi was killed in the Libyan uprising, the plane was flown to the southwestern French city of Perpignan, where it underwent three million euros' (USD 3.36 million) worth of repairs and maintenance by an Air France sub-contractor.
Its withdrawal brings the battle to a close.
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"We have preferred to focus on the seizure of other Libyan assets, which will be more feasible," Al-Kharafi's French lawyer, Remi Barousse, said.
In 2006 Al-Kharafi signed a contract with the Kadhafi regime to build a beach resort on Libya's Mediterranean coast, which it was to run for 90 years, but Tripoli cancelled the deal unilaterally in 2010.
A Cairo court in 2013 ruled Al-Kharafi was owed USD 937 million (835 million euros) over the broken contract and the company filed to seize the plane to recover some of the money.
In November 2015, a Perpignan court ruled that the plane had immunity from seizure as it was state property.
Kadhafi was killed in October 2011, after which the oil-rich country slid into chaos, with the Islamic State group making inroads.
A unity government was set up in Tripoli in late March after a UN-backed agreement in Morocco in December 2015.
But it has struggled to assert its authority across the country, facing opposition from a rival government in the east.