Stade Francais ensured Clermont's dire record continued as the Paris club handed the side from central France their 11th defeat in 12 French finals.
South Africa fly-half Morne Steyn kicked Stade Francais into a 6-0 lead, while Morgan Parra missed two chances to reduce the lead for Clermont.
Steyn added a third penalty before Camille Lopez made it 9-3 at the break.
Brock James cut the gap to three but missed a chance to level the scores and Steyn added a fourth penalty late on.
It was the second defeat in a final this season for Clermont, who lost the Champions Cup final to Toulon in May - the second time in three years the Mediterranean club have beaten the Vulcans to become European champions.
"Once again we lose - we have this horrible reputation," said Clermont captain Damien Chouly. "There's an anger we feel towards ourselves, what with history repeating itself."
In contrast, Stade Francais captain Sergio Parisse said "it's just a dream".
"It wasn't a great final to watch, but we don't care, we dealt with it and we let nothing go," added the Italy number eight.
It was a nervy and low-scoring encounter, which was ultimately decided by the power of the Stade Francais scrum, and the greater accuracy of their kicker Steyn.
Clermont were missing France's Wesley Fofana and Wales' Jonathan Davies in the centres through injury and, with their midfield attacking threat duly blunted, they rarely looked like breaking down the powerful Stade Francais defence.
With the Vulcans trailing by three points inside the final 10 minutes, former England full-back Nick Abdendanon's counter-attack saw him beat a handful of men and take Clermont into the Stade Francais 22.
But when the ball was recycled, giant Fijian wing Napolioni Nalaga was bundled into touch five metres out.
Clermont still had a chance to level the scores but James missed an angled penalty to end their challenge and Steyn's fourth kick made certain of the win for Stade Francais.