As well as Mamluk, the warrants name Syrian Air Force intelligence chief Jamil Hassan and Abdel Salam Mahmud, the head of Air Force intelligence in the Damascus district of Bab Tuma.
They are the first international arrest warrants issued by French officials for officials from President Bashar al-Assad's state apparatus.
The accusations arise from the cases of student Patrick Dabbagh and his father Mazen, who worked at the French school in Damascus.
Both had joint French and Syrian nationality.
They were arrested in November 2013 by men claiming to be from air force intelligence and transferred to the al-Mezzeh prison, which is reported to be a torture centre.
Their arrest came to light due to the revelations of a former Syrian military photographer who fled the country in 2013 with 55,000 photographs of alleged victims of torture.
A preliminary inquiry was opened in France in 2015 and one of Mazen Dabbagh's brothers joined rights groups in filing a civil complaint in 2016.
The Syrian authorities declared the pair were dead this summer, leading investigators to include voluntary homicide to the list of accusations against the Syrian officials.