Verdon was taken from a hotel in northeastern Mali in November 2011 by Al-Qaeda in the Islamic Maghreb (AQIM) while on business, as was Serge Lazarevic, another French national.
Relatives and loved ones gathered in a private room at Paris's Charles de Gaulle airport to retrieve the body, which was flown back on an Air France plane that landed around 0700 GMT, the source said.
The 53-year-old's captors announced in March they had killed him but Paris had never confirmed this until his body was discovered in the country's north and identified this month.
The French foreign ministry announced Sunday that Verdon's body had likely been found at the beginning of July, and President Francois Hollande later confirmed the tragedy.
Verdon suffered from an ulcer and tachycardia, an abnormally fast heartbeat, when he left for Mali in 2011.
"For us, it's possible that Philippe died because of his illnesses and that AQIM used this and staged (a killing)," said Pascal Lupart, head of a support committee for Verdon.
An autopsy will take place to determine exactly how he died.
French forces intervened in Mali in January to help the weak Malian military drive out Islamist rebels who had seized control of the country's north, angering extremists
At least seven French citizens remain captive in Africa, with another two in Syria.