Fabio Grosso's team continues to struggle without a win in nine league matches this season, accumulating a mere three points amidst a turbulent few months.
Before halftime, the hosts found themselves trailing by two goals, courtesy of strikes from Muhammed Cham and Yohann Magnin, propelling Clermont towards their first victory of the season.
An own goal from Florent Ogier early in the second period gave Lyon hope, but they could not find an equaliser and are now the joint-lowest scorers in the division with Clermont on just seven goals.
Lille beat Brest 1-0 with an early goal from Yusuf Yazici which saw them climb above their opponents into fourth on goal difference.
Elsewhere, Toulouse and Reims played out a 1-1 draw, while Nantes saw off Montpellier 2-0.
On Saturday, PSG cruised past Strasbourg 3-0 and Nice edged out 10-man rivals Marseille 1-0.
