Despite going up at half-time, the Girondins were deflated by a resurgent Phocaens in the second half at Stade Velodrome.
After a dreary start to the game, Yacine Adli put the visitors ahead in the 31st minute after profiting from a one-two by Nicolas de Preville and Josh Maja to rifle past Steve Mandanda.
However, Marseille woke from their slumber in the second half to secure maximum points thanks to goals from Jordan Amavi, Morgan Sanson and Nemanja Radonjic.
Maja, who got his first career hat-trick against Nimes, saw every minute of action but could not prevent Paulo Sousa’s side from surrendering their five-match unbeaten run.
Bordeaux are fifth in the log with 26 points from 17 league outings, while Andre Villas-Boas’ men occupy the second spot with 34 points.
Kalu and Maja are expected to be in action in their next outing against Strasbourg on December 15.