The only goal of the game arrived three minutes before half-time through Ivan Santini’s penalty.
The spot-kick was awarded when Nice’s Malang Sarr lost possession, allowing Ronny Rodelin to surge into the box where he went down under Dalbert’s challenge.
Santini sent Yoan Cardinale the wrong way from 12 yards and that proved enough for victory in a match that saw Nice record only one shot on target.
Having picked up 29 points from their first 11 games, the 1-0 away reverse means their lead over Monaco at the top of the table has been cut to three points over the course of the weekend.
Champions Paris Saint-Germain can also move to within three points of Lucien Favre’s men if they defeat Rennes later on Sunday.
Caen’s win sees them jump from 18th to 15th in the table after 12 matches.