The French Ligue 2 club appointed the 36-year-old on Wednesday, making her the first female boss of a French men's team.
Costa has previously coached Benfica's youth teams and has also spent time in charge of the women's sides for both Qatar and Iran.
The Portuguese, who served as a scout for Celtic between 2008 and 2011, will take over at the Stade Gabriel Montpied at the end of the season, and Blatter was quick to hail the decision as a positive step for the game.
Blatter posted on his Twitter account: "Congratulations and good luck to Helena Costa @ClermontFoot. Great news for women in football today."
Those sentiments have been echoed by the French government, with women's minister Najat Belkacem also praising the club for their actions.
"Bravo Clermont Foot for understanding that giving a place to women is the future of professional football," Belkacem stated on Twitter.
Earlier Clermont said that the aim of the appointment is to "help the club enter a new era".
The second-tier team have endured a disappointing season in Ligue 2 this term, and sit 14th - six points clear of the bottom three - with two games to play.
