Angers, who had not won at the Stade Velodrome since 1978, prevailed thanks to goals by Thomas Mangani, a penalty, and Romain Thomas. Michy Batshuayi reduced the deficit with a late spot-kick for Marseille.
The result lifted Angers to fifth place with 15 points from eight games while Marseille, who have lost four league matches, are 14th on eight points.
OM Coach Marcelo Bielsa resigned after the first game and their fortunes have not improved.
Following crowd trouble during a 1-1 draw against Olympique Lyonnais last weekend, the North and South stands of the Velodrome had been closed after a preliminary ruling by the French League (LFP).
The sanction is likely to get heavier when the LFP's disciplinary committee makes a definitive ruling on Oct. 15 after OM fans threw glass bottles on to the pitch last Sunday, causing a 23-minute game interruption.
Angers got off to a solid start with Fode Dore proving a dangerous threat to the Marseille defence.
In the 37th minute, Remy Cabella fouled Arnold Bouka Moutou in the area and Magani converted the resulting penalty.
Marseille stepped up a gear after the interval but Ludovic Butelle made a couple of superb saves to deny Batshuayi and Bouna Sarr.
The visitors, however, doubled their lead in the 70th when he headed home from Billy Ketkeophomphone's cross from the left.
Marseille cut the deficit 11 minutes from time when Batshuayi beat Butelle from the spot after Lucas Ocampos had been fouled in the box.
Monaco let a one-goal advantage slip three times in a 3-3 draw at En Avant Guingamp as Nicolas Benezet, who scored a double, struck late to deny the principality side a second victory in a row.
Bernardo Silva, Andrea Raggi and Nabil Dirar found the back of the net for Monaco but Sloan Privat and Benezet, who scored the equaliser in the 89th, cancelled out the visitors' lead.
Monaco are eighth on 12 points.
Later on Sunday, second-placed St Etienne will narrow the gap on leaders Paris St Germain to one point if they beat Nice at home.
(Reporting by Julien Pretot; Editing by Ed Osmond)
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