Jose Callejon's first-half strike was followed by Duvan Zapata's first goal for Napoli and give them the breathing space they needed following Andre Ayew's late strike.
Victory for Rafa Benitez's side meant they drew level with Borussia Dortmund and Arsenal, after the German side's 2-1 win in London.
Napoli welcomed back summer signing Gonzalo Higuain from a hamstring injury but it was fellow attacker Dries Mertens who was at the heart of the visitors' early threat.
The Belgian forced Steven Mandanda to keep out his early free-kick before angling a shot wide.
Benoit Cheyrou passed up a presentable chance for Marseille while Dimitri Payet's ambitious effort never threatened the target.
Napoli should have taken the lead after 35 minutes when Higuain spurned a gilt-edged chance after he and Mertens had been sent one-on-one with OM goalkeeper Mandanda.
Higuain made Napoli's opener on 42 minutes though when his hooked pass caught the home defence out.
Callejon was on the striker's wavelength and burst forward to chest the ball down before cutting inside and firing in his low shot.
Napoli continued to be in control of the match after the break and were twice appealing for penalties.
The ball appeared to make contact with Cheyrou's hand in the penalty area only for the referee to wave away appeals before Mertens went down in the area.
Higuain made way for Zapata and the Colombian made an almost instant impact.
Marek Hamsik's clever back-heel afforded him just enough space to get a shot off on the edge of the area and with the aid of a deflection the ball beat Mandanda.
Marseille grabbed a lifeline into the game with five minutes left when the Ayew brothers combined.
Jordan teed up his brother Andre who caught Pepe Reina slightly off guard with a first-time finish that flew into the corner.
No equaliser was forthcoming though as Marseille's hopes of qualification were almost certainly ended.