The London club led 12-0 after two early tries and looked in control but Clermont fought back to ensure there was only a point in it going into the last 10 minutes.
Saracens, however, as they have so many times before, held their nerve under pressure as Alex Goode broke through for the killer third try in the 73rd minute which Owen Farrell crucially converted from the touchline.
The victory made Saracens the fourth team to retain Europe’s premier club title after Leicester, Leinster and Toulon while perennial bridesmaids Clermont, who have lost 11 of their 12 French championship finals, became the first to play in three finals and lose them all.
"It was an incredible performance and it needed to be." said Saracens director of rugby Mark McCall. "We just couldn’t get away from them. I felt we had a lot of pressure and were dominant in a lot of areas but then it was a one-point game.
"After they scored that unbelievable 100-metre try we had to show our experience and resilience and I'm really pleased with the way we attacked and went after them in that last 20 minutes."
Against a backdrop of deafening noise and colour, Saracens roared out of the blocks and only a desperate tackle by Nick Abendanon prevented Chris Ashton scoring after 90 seconds.
But the Toulon-bound former England winger was not denied for long as 11 minutes later he ran on to a chipped kick by Goode to gather and dive over to become the tournament’s all-time leading scorer with 37 tries.
With man-of-the-match Billy Vunipola in irresistible form, the holders looked in total command and stretched the lead to 12-0 when lock George Kruis charged over following more good work by Goode.
Clermont, however, gathered themselves and working tirelessly through their forwards sent Remi Lamerat over for what was the first first-half try Saracens had conceded in the competition all season.
Relentless pressure
Morgan Parra converted and it stayed 12-7 at the break.
Farrell extended it with a penalty but Clermont, with a succession of breakdown turnovers, got back to within a point when Abendanon finished a brilliant move that started in front of their own posts with Scott Spedding making ground and then another break and offload by Peceli Yato. A penalty apiece for Farrell and Parra meant it was 18-17 heading into the last 15 minutes with the tension palpable.
Saracens gradually tightened the noose though and their relentless goalline pressure eventually opened the way for Goode to score their third try seven minutes from time.
The ice-veined Farrell made it a vital eight-point lead, which looked decisive and became so a minute later when Camille Lopez missed an easy penalty at the other end.
Saracens will now turn their attention to trying to complete the double-double - they face Exeter away in the Premiership semi-finals next week.
Clermont, beaten by Toulon in the 2013 and 2015 finals, will have to regather for another assault on the French championship, where they currently lie second.
"We are absolutely gutted. We don't know what we're missing but hopefully one day it turns our way," said Spedding.
Abendanon said he would have put his mortgage on Clermont victory, such was the belief in the camp this week.
"When it was 17-18 I thought we were going to do it but unfortunately again it hasn’t gone our way," said the Englishman.
"It's not a nice feeling to be the first to lose all three finals – we’ve just got to hope that next year’s going to be our year."