Around 200 soldiers of the 25th Belfort infantry regiment, responsible for overseeing the hastened French exit from the 11-year war, took off around 2:30 pm local time (1000 GMT), an airport official told AFP.
They are expected to return to France on December 18 following a three-day decompression stay on the Mediterranean island of Cyprus.
Their departure means France has around 1,500 soldiers left in Afghanistan, the vast majority in Kabul. They are due to stay into 2013 to take responsibility for repatriating equipment and training the Afghan army to take over.
After then, only several hundred French soldiers involved in cooperation or training missions will remain in the country.
At the height of its involvement, France had 4,000 soldiers in Afghanistan as the fifth largest military contingent in the International Security Assistance Force (ISAF), behind the United States, Britain, Germany and Italy.
France joined the NATO coalition in late 2001 to help prop up the new government against an insurgency, which began after a US-led invasion toppled the Taliban government earlier that year for giving refuge to Osama bin Laden and his Al-Qaeda network, following the 9/11 attacks on New York and Washington.
In 2007, the French moved into the strategic province of Kapisa, which straddles the transit route from Kabul to Pakistan, after president Nicolas Sarkozy agreed to an American request to take on more of the fight against the Taliban.
What followed was an increasingly bloody fight against insurgents and armed groups.
After a series of attack, notably in January when an Afghan soldier shot dead five French troops, Sarkozy announced that the combat mission in Kapisa and the district of Surobi would end in 2013.
His successor Francois Hollande fast tracked that to the end of 2012, initially to veiled criticism from US officials, and the last French combat soldiers left Kapisa and returned to Kabul on November 20.
Insider attacks have spiralled this year, with 61 NATO soldiers killed by Afghan security personnel, fuelling distrust in the war against the Taliban.
The attacks have led to calls in other Western countries, where the long war is increasingly unpopular, for early troop withdrawals. But NATO has insisted it will follow the agreed programme of pulling out all combat troops by the end of 2014.
French and Afghan commanders say Kapisa stabilised but two out of its six districts are thought to be at least partly controlled by insurgents.
Security in the province is now the responsibility of 4,700 Afghan police and soldiers, supported by 250 American soldiers.
France is not the first country to end its combat mission.
Canada did so in July 2011 and the Netherlands in August 2010.
The United States pulled out 33,000 "surge" troops earlier this year, although it still has some 68,000 soldiers serving in Afghanistan.
France has lost 88 soldiers in Afghanistan.