Clermont, bonus point victors over the Welsh team last weekend, repeated that feat after refusing to be blown off a quarter-final course in wet and windy Llanelli as wing Napolioni Nalaga's double and Fritz Lee's touchdown complemented a 60th-minute penalty try.
Mike Delany kicked a penalty and conversion, while Brock James added three conversions for a 31-13 success.
The Scarlets did not score a second-half point after leading 13-10 at the break through centre Gareth Maule's try, plus eight points from fly-half Rhys Priestland's boot.
The victory means Clermont are eight points clear of second-placed Harlequins, who host Racing Metro on Sunday.
Clermont were without injured international backs Morgan Parra, Wesley Fofana and Lee Byrne, but they still arrived in west Wales boasting an outstanding Heineken pedigree after finishing as runners-up last season and semi-finalists in 2012.
The visitors' line-up featured former Scarlets centre Regan King, who will return to Llanelli next season as replacement for Clermont-bound Wales star Jonathan Davies. King partnered Clermont captain Aurelien Rougerie in midfield.
Despite wet and windy conditions, Clermont took just 17 seconds to make their mark on the contest as they claimed one of the quickest tries in Heineken Cup history.
Scrum-half Thierry Lacrampe's precision kick into opposition territory was caught at full tilt by Nalaga, and he crossed wide out before Delany made a mockery of conditions by landing the touchline conversion attempt.
It was a crushing blow for the Scarlets, and they showed little sign of recovering their poise when Priestland drifted a fifth-minute penalty chance wide.
But Priestland's 23rd-minute penalty cut the deficit, awarded by referee Wayne Barnes after Rougerie was sin-binned for throwing a punch at Wales centre Scott Williams.
Rougerie and Williams got to grips with each other after Scarlets flanker Josh Turnbull mercilessly cleared Lacrampe from a ruck, sparking a dust-up between several players, but it was Rougerie who was singled out.
The Scarlets had coped well with Clermont's all-action game, and they stung their opponents eight minutes before half-time through a brilliant 70-metre try.
Williams, whose counter-attacking instincts were never far from the surface during Wales' recent autumn Tests, scattered Clermont's defence with a weaving run, before full-back Liam Williams and Priestland served as critical links, enabling Maule to touch down.
Priestland added the conversion and then kicked his second penalty as Clermont displayed signs of being rattled when lock Jamie Cudmore needlessly infringed through a late challenge on Scarlets number eight Rob McCusker.
The combined effect represented a concerted Scarlets fightback following Nalaga's early score, although a Delany penalty made it 13-10 at the break, his strike arriving after the officials missed a blatant stamp from Clermont flanker Julien Bonnaire which could attract the citing commissioner's attention.
Delany made way for James early in the second period, but Clermont's normally outstanding goalkicker missed two straightforward penalty chances in as many minutes as his team looked to build pressure.
There were also increasing signs of the Scarlets scrum struggling under pressure, with Clermont needing no second invitation to turn the screw, sacrificing two kickable penalties in favour of seeking a penalty try through their set-piece domination.
Barnes finally went between the posts after issuing a general warning to Scarlets skipper Phil John, with James converting the penalty try that put Clermont four points in front.
Williams then had a kick charged down by Clermont's former Scotland lock Nathan Hines, and Hines' fellow substitute Lee touched down, with the try confirmed following lengthy deliberation by television match official David Grashoff.
James' conversion took the visitors 11 points clear, and there was no way back for a Scarlets team high on endeavour and effort, but lacking Clermont's control and organisation at key moments as Nalaga's second try secured a five-point maximum.
- Sports & Recreation
- Rhys Priestland