Morgan Parra masterminded back-to-back wins for Clermont over the champions, slotting eight of his nine kicks at goal for a 23-point haul.
Leinster are now eight points adrift of their opponents, who lead the way in Pool Five.
A crowd of 48,964 - an Irish record for a European pool match - watched Wesley Fofana cross for a try five minutes before the break to help Clermont push 16-6 clear.
Man of the match Parra managed to convert Fofana's try, adding to three earlier penalties, with Jonathan Sexton booting a brace of penalties for the Irish province.
As Leinster continued to leak penalties, Parra kept Clermont on course to end a run of five straight defeats in Ireland since 2007.
The margin was widened to 25-9 before Leinster recovered to score two tries in the closing quarter-hour through Shane Jennings and Fergus McFadden, the latter's effort coming in a daring last-minute raid that garnered a losing bonus point for the hosts.