Marseille, thrashed 3-0 at Real Madrid in the Champions League on Wednesday, paid dearly for a poor first half.
Monaco, who proved sharp on the break, moved up to fourth in the standings with 15 points from eight games with Marseille slipping to fifth.
Olympique Lyon led the table on 20 points after beating RC Lens away on Saturday.
"It is the worst week we could imagine," said OM coach Didier Deschamps whose side were also beaten by Valenciennes in Ligue 1 last weekend.
"For the moment, it's not working but I am convinced my team are able to do much better than what they did this week."
At the Stade Velodrome, Nene opened the scoring with a free kick from the edge of the box that took a deflection off Lucho Gonzalez's head in the 20th minute.
The visitors doubled the tally on 41 minutes when Park Chu-young outpaced the Marseille defence on the break to fire the ball past a helpless Steve Mandanda.
Monaco found themselves under high pressure shortly after the hour with a Bruno Cheyrou strike smashing the woodwork and keeper Stephane Ruffier tipping a Stephane M'Bia header over his bar.
Senegal striker Mamadou Niang pulled one back with four minutes left, flicking the ball past Ruffier after being perfectly set up by Hatem Ben Arfa.
Earlier, Toulouse lost 1-0 at home to FC Lorient in Ligue 1 in a game marked by an emotional tribute to their fan who died this week.
In an emotional pre-match ceremony, Lorient and Toulouse players laid a wreath before the East curve in memory of Brice Taton, who passed away on Tuesday after being beaten by Partizan Belgrade fans at a Europa League game on Sept. 17.
The fans held a one-minute round of applause before kick-off.
Both teams failed to find their range until the 88th minute, when Olivier Monterrubio converted a penalty kick following a handball in the box by Etienne Didot.
Pierre-Alain Frau struck twice to give Lille a 3-2 win at promoted Boulogne.
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