Needing a win to haul in La Rochelle, which had beaten Castres 24 hours earlier, Clermont went one better at Stade Marcel-Michelin by securing a bonus point to move ahead of its rival.
After Pierre Bernard opened the scoring with an early drop goal, the host forged a healthy lead as Camille Lopez's 24th-minute touchdown was followed up by a penalty try at the end of the first half with Toulon's Liam Gill in the sin bin.
Clermont lost Viktor Kolelishvili to a yellow card three minutes after the interval, but Toulon could not capitalise and a controversial score from Wesley Fofana put the result beyond doubt.
Fofana intercepted a James O'Connor pass to race clear, before being tackled by Bryan Habana as he looked to ground the ball. Replays suggested Fofana had not cleanly grounded the ball, yet the try was awarded and Remi Lamerat added another with eight minutes remaining.
Stade Francais suffered a first home defeat of the season as two late tries from Yoann Huget sealed an unlikely 18-15 victory for Toulouse at Stade Jean-Bouin.
Trailing 15-3, the visitor was given hope when Paul Gabrillagues was yellow-carded with 17 minutes remaining.
Huget was driven over for his first score eight minutes later to ensure Toulouse made the most of its numerical advantage, and a second try followed almost immediately for the France winger - after a blistering break from Maxime Medard - to leave Stade stunned.