A French court on Monday passed the sentence on special forces soldier Sébastien L, 40, and banned him exercising an occupation that would bring him in contact with children.
The offence took place in 2015 when he was in Burkina Faso as part of France's operation in the Sahel.
While staying in a Ouagadougou hotel, a French-Burkinabé woman found video of the man abusing her daughter and another girl, one aged three, the other five, in the swimming pool and complained to the French embassy.
The soldier at first denied the charge but later confessed, blaming the effects of alcohol and the stress of his work.
The court also ordered him to pay compensation - 6,000 euros to one girl and 3,000 to her mother, 4,000 to the other and 2,000 to each of her parents and 1,000 euros to each of the grandparents.
Investigators found no case against another soldier who was with Sébastien L at the time.
The case became public two months after allegations of sex abuse of minors by French soldiers in the Central African Republic (CAR) were published in the British press.
Prosecutors asked for the charges to be dismissed in that case but another investigation into alleged child sex abuse by soldiers in eastern CAR is still under way.