It means she becomes the first female coach to manage a team in the men's professional game in world football.
Helena, who was most recently coach of the Iran women's team, scouted for Celtic in Portugal and Spain.
The Portuguese coach will officially take up her new role at Clermont Foot at the end of the season in France.
A spokesperson for Celtic said: "We would like to congratulate Helena sincerely on taking up this new role.
"She did an excellent job for us and we know she will give her new position the same high level of commitment and dedication which she gave to Celtic."
Clermont Foot striker Remy Dugimont said he was pleased with the arrival of the 36-year-old, adding: "We learned together this morning.
"We were told the new coach was this lady. It is a surprise, a big surprise, because a lot of names were circulated; all coaches who were more or less unemployed.
"It came out of nowhere and now we have to get to know. It is good, it will create a buzz and will be a unique experience.
"I'm not macho. She has worked in the profession and all the boys know how it works.
"At first it will be a little weird but it will only last a few days. We don't not know who chose to bring her, we hope it will be okay."