Marcelo Bielsa's team - who had given up winning positions to draw their last two league games 2-2 - looked on course for a comfortable win when Andre-Pierre Gignac came off the bench to put them two to the good just after the hour mark.
Victory would have lifted Marseille to within a point of table-topping Lyon, but Caen had other ideas, as Nicolas Seube and Emiliano Sala drew them level within seven minutes of Gignac's goal.
And substitute Benezet was on hand to complete a remarkable comeback three minutes from time, as he cut in from the left and rifled an unstoppable drive beyond Steve Mandanda and into the far top corner.
Caen were 2-0 down with just two minutes remaining at champions Paris Saint-Germain a fortnight ago - and Patrice Garande's in-form side once again displayed their powers of recovery to deny Bielsa a vital three points.
Marseille had a golden opportunity to take the lead after just three minutes, but Michy Batshuayi had a penalty saved by Remy Vercoutre after he had been fouled in the box by Alaeddine Yahia.
Buoyed by Vercoutre's save, Caen twice went close as first Emmanuel Imorou had an effort cleared off the line, before Sala had an excellent shot tipped onto the bar by Mandanda.
But it was Marseille who broke the deadlock in first-half injury time, when Andre Ayew converted the rebound after Vercoutre had saved Dimitri Payet's shot.
Sala was again unfortunate not to find the net early in the second half when Benjamin Mendy cleared his close-range shot off the line, and he was punished for that bad miss when Gignac found the net just four minutes after replacing Batshuayi.
Caen refused to buckle, though, and drew themselves level within seven minutes through Seube and Sala.
And there was to be one more twist in the tale, as Benezet earned the visitors a sensational victory with a goal worthy of winning any game.
