Goalkeeper Gennaro Bracigliano, who will deputise for the suspended Steve Mandanda when Marseille take on Bayern Munich at the Stade Velodrome in a Champions League quarter-final next week, failed to deal with a high ball, allowing Johan Christophe Ayina to poke the ball into the empty net in the 119th minute.
Marseille, who dropped to ninth in Ligue 1 after five consecutive defeats, twice came from behind thanks to France striker Loic Remy but Bracigliano's blunder cost them a place in the last four.
At Caen's Michel d'Ornano stadium, where the game was played to allow more fans, a minute's silence was observed before kick-off in memory of the seven people killed in three separate shootings in one week in Montauban and Toulouse.
Marseille came close shortly before the break but Issa Coulibaly pulled off a lightning-quick save to punch away Rod Fanni's deflected cross.
