Vital N’Simba drilled in from 20 metres just after the half-hour to earn Clermont a first victory in eight matches and deny Lille the chance to break into the top three.
Lille president Olivier Letang had harsh words after watching his champions slip to a fourth league defeat in 10 matches under new coach Jocelyn Gourvennec.
“With individual and collective poverty you can’t hope to compete at the top level,” he said with Lille’s title defence looking compromised as they sit ninth, 13 points behind runaway leaders Paris Saint-Germain.
“We hit the bottom, we were really bad.”
Lille struggled in the absence of the suspended Burak Yilmaz, with top scorer Jonathan David limited to 20 minutes off the bench after returning late from World Cup qualifying duty with Canada.
Portugal defender Jose Fonte had the best chance for Lille in the closing stages but shot straight at Clermont goalkeeper Arthur Desmas.
Gourvennec said defeat had been a shock that could provide a wake-up call.
“Well done to them, they played it like a cup game,” he said.
“Now we have to turn this general disappointment from the players and the president into a revolt.”
Karl Toko Ekambi continued his good form by breaking the deadlock with a 75th-minute penalty — his fourth goal in seven games for Lyon.
Peter Bosz’s men wrapped up the points in the 90th minute as Belgium centre-back Jason Denayer scored following a brilliant no-look pass from midfielder Lucas Paqueta.
Former AC Milan player Paqueta had been in action for Brazil less than two days earlier during their 4-1 World Cup qualifying win over Uruguay, over 8,000km away in Manaus.
“It’s important to get points to move up the standings,” said Lyon defender Jerome Boateng, who joined in the close-season after 10 years at Bayern Munich.
“I feel better and better in the league, the team. My understanding with Jason Denayer is improving. He’s a good player with whom I form a good duo.”