Gourdel, 55, had been hiking in a national park that has increasingly become a haven for militants when he was kidnapped by extremists with the Jund al-Khilafa (Soldiers of the Caliphate).
The kidnappers said Gourdel was taken in retaliation to France’s air strikes against the Islamic State group in Iraq.
A video posted online showed him being beheaded two days later on September 24.
The Algerian army mobilised some 3,000 troops to search for Gourdel’s body and eventually were led to it from a tip of a detained suspected militant, according to officials.
Gourdel’s body was later found in a booby-trapped grave in the Kabylie region, east of Algeris, on January 15.
A source close to the case told AFP on Sunday that Gourdel’s body will now be flown back to France.
Gourdel’s sister had also flown to Algiers with two French pathologists to help identify his body and obtain a death certificate.
Abdelmalek Gouri, the man who claimed responsibility for Gourdel's death and leader of the Jund al-Khilafa, was killed in an Algerian army attack 50 kilometres east of Algiers in December.