Tries from Fiji centre Noa Nakaitaci, scrum-half Thierry Lacrampe and left-wing Julien Malzieu handed Clermont just their second win on the road this season, and their first since the opening day of the campaign.
Wales international James Hook added two conversions and three penalties to complete the scoring for the title favourites, while the home side earned a bonus point thanks to a penalty try and a try from winger Sofiane Guitoune.
"It's an interesting and important win," said Clermont manager Vern Cotter.
"It's come at the right time because we have back-to-back matches against Scarlets (in the European Cup) from next weekend.
"It's important because we wanted to test ourselves away from home."
Perpignan manager Marc Delpoux was left to rue the defeat, which he felt was undeserved.
"I'm disappointed because we had the game in our hands," he said.
"The match turned on some difficult facts. We had five players go off injured during the match."
The rest of the round's fixtures will be played over the weekend.