Defending champions Castres brought Clermont's four-year 77-match winning home run to a shuddering halt Saturday as a 22-16 victory took them into the French Top 14 rugby semi-finals.
South African scrum-half Rory Kockott played a central role kicking 17 points and setting up his side's only try.
Castres will face Montpellier in the semi-finals next Saturday.
Defeat brought an end to New Zealander Vern Cotter's eight-year reign as coach of Clermont as he now tries to revive the Scottish international team.
It was Clermont's second successive shattering defeat in the space of two weeks after they had been knocked out of the European Cup in a 46-6 semi-final rout by Saracens.
"Nobody expected us to win here but we believed in what could happen," said Castres coach David Darricarrere.
"This team is at its strongest when no-one expects us to do well."
Clermont skipper Aurelien Rougerie admitted that an era was coming to an end at the club.
"We are disappointed but Castres took their chances and were better in the basics," he said.
On Friday, Irish international fly half Jonathan Sexton kicked seven penalties from seven attempts to give Racing-Metro a 21-16 win over Toulouse in their quarter-final.
Defeat meant Toulouse's run of 20 successive semi-final appearances came to an end while Sexton's perfect display handed Racing a first ever last-four date and a clash with European champions Toulon next weekend.
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