Marseille piled more pressure on Chelsea's under-fire coach Carlo Ancelotti as a second-half goal from Brandao brought the Blues' unbeaten Champions League run to an end.
Having already won Group F, Chelsea were lethargic and passionless despite Ancelotti's call for a return to the free-flowing football they produced in abundance at the start of the current Premier League season.
Although the game had nothing riding on it apart from pride, the English champions looked a pale shadow of the side that took defences apart with ease for most of last season.
The Blues have now recorded just two wins out of their last eight games in all competitions and the storm clouds will continue to gather over Ancelotti until they reverse their alarming slump.
Marseille started brightly and almost took the lead in the seventh minute, but Benoit Cheyrou's volley from 20-yards flashed just wide of the post.
It certainly was not the entertaining start Carlo Ancelotti had wanted from his side.
Only the woodwork saved Chelsea when Mathieu Valbuena rattled the crossbar with a 20-yard drive that had Petr Cech beaten.
Moments later Loic Remy flashed another long-rage effort just wide and Brandao put another shot on the turn inches wide of the upright as Chelsea looked extremely vulnerable in defence.
There was total confusion when Chelsea appeared to have been awarded a penalty by Russian referee Vladislav Bezborodov after Souleymane Diawara brought down Florent Malouda.
The Russian pointed to the spot but, under pressure from Marseille players, appeared to consult his linesman and change his mind. He then awarded the Blues a corner instead, much to the annoyance of the Chelsea players.
Marseille had a 'goa'l ruled out for offside in the 35th minute when Gabriel Heinze was adjudged to have slipped offside from Cheyrou's free-kick.
Heinze rose unchallenged to head home from six yards but was immediately flagged offside by the referee's assistant.
It was the home side who again looked the more threatening after the break but although they pinned Chelsea down in their own half, the final ball was lacking.
Didier Drogba, who had looked distinctly out of sorts all evening, was eventually replaced on the hour by Daniel Sturridge.
The deadlock was broken in the 81st minute when Taiwo's cross-shot was deflected into the patch of Brandao and he tucked the ball home from six yards.