The two men, aged 36 and 38, arrived in France on Thursday morning and were immediately taken into custody.They had already been interrogated by French and Burkinabé police after being arrested on Wednesday.
A Franco-Burkinabé woman has accused them of sexually assaulting her two girlss, aged three and five, in a hotel swimming pool on Sunday.
The woman, who is the mother of the younger girl, invited the two to her home for a drink.
One of them left a Go Pro camera behind and she allegedly found a "fairly long" film of the sex abuse.
"There was a soldier who filmed the scene with a camera while the second touched [the girl]," a senior police officer in Burkina Faso told the AFP news agency.
The mother took the film to the French embassy and it was later seen by the father of the other child.
Paris prosecutors opened their investigation on Tuesday, while the defence ministry said the military was also looking into the allegations.
"Even though they benefit from the presumption of innocence, the information we have makes the accusations against them seem highly probable," said defence ministry spokesperson Pierre Bayle, stressing that both men were immediately suspended.
Allegations of paedophile sex abuse by French troops in the Central African Republic were revealed in the British press in April.