"The death of our compatriot Mr. Philippe Verdon is formally confirmed," Xinhua cited the president as saying in a statement.
Hollande expressed solidarity to the family and loved ones of the victim, and vowed to identify those responsible for the death of Verdon and bring them to justice.
The remains will be transferred to France and autopsies will reveal the cause of his death, said Hollande.
The president made a pledge to those families "whose loved ones are still being held hostage in the Sahel" that his government continues to "fully mobilize for their release and return to France".
"All government departments are keeping work and no track is ignored or overlooked," the president added.
On Monday, Hollande revealed that a body was found 10 days ago in northern Mali which is believed to be that of Verdon, who was killed by his kidnappers.
He said "additional checks" were underway, including a DNA analysis to authenticate the remains.
Verdon was kidnapped during the night of Nov 24, 2011, together with Serge Lazarevic. They were on a business trip for a cement project, and were abducted from their hotel in Hombori.
In March, an al-Qaeda spokesman told Mauritanian news agency ANI that Verdon was executed in response to France's military intervention in Mali.
At the beginning of 2013, the French army was engaged in a military operation in support of Mali's army against armed Islamist groups in northern Mali.
So far, five French people have been taken hostage in Sahel region.