Andre Gagnon, 48, was on trial for the alleged sexual assault of then-corporal Stephanie Raymond in December 2011 at an armoury near Quebec City.
His court martial was overseen by a colonel in front of a panel of five male soldiers who reached the verdict.
Gagnon's lawyers said the sex was consensual, while the Crown argued that he used his superior rank to coerce Raymond, 30, into carnal acts.
One of Raymond's lawyers, Lt.-Col. Marylene Trudel, accused Gagnon during the court martial of using her client as an "open bar'' for his sexual gratification.
Gagnon faced one count under Sec. 130 of the National Defence Act as well as the Criminal Code section corresponding to sexual assault.
Raymond, who served under Gagnon, testified that he made advances, engaged in sexual touching and attempted to get oral sex after a holiday party.
Raymond, who was not present for the verdict, said she initially went along with his actions because she feared later reprisals.
The panel did not give reasons for its verdict, but Maj. Philippe-Luc Boutin, who defended Gagnon, said his client testified in a very clear and precise manner.
"He didn't try to hide or diminish his own involvement in the sexual exchange that was carried out," Boutin said.
"At the end of the day, I don't think Ms. Raymond had the same approach. She was very evasive on many issues . . . so the jury, I think, had serious doubts about the truthfulness of her story."
Raymond's lawyers said they will review the evidence and decide whether to appeal the verdict within 30 days.
"The Crown can appeal the decisions of a court martial when there is a solid chance of success and it is in the public interest to do so," said Trudel.
Raymond, who insisted her name not be protected under a publication ban, filed a complaint against Gagnon and was subsequently discharged by the army.
Gagnon testified that Raymond was the initiator in the December 2011 incident and straddled him when they were alone in a room at the Regiment de la Chaudiere armoury in Levis after the party, where there had been considerable drinking.
He said she consented to sexual activities that included fondling, kissing and receiving oral sex. Gagnon said she only objected when he attempted to penetrate her and that he stopped at that point.
Gagnon testified that Raymond agreed to join him to sit on the floor of an empty room at the armoury to "relax and sober up.'' It was at this point, he said, that she straddled him.
He said he interpreted this as an expression of openness and that Raymond remained passive and did not return any of the sexual touching.
The proceedings were handled by a court martial because both Gagnon and Raymond were in the Canadian Forces at the time of the incident. Raymond is now a full-time student.
The case was also under military jurisdiction because the alleged crime happened at a Canadian Forces installation.
Gagnon faced a maximum of 10 years behind bars had he been convicted.