The French side stunned their hosts early on when Andre Ayew opened the scoring, but goals from Gokhan Inler and Gonzalo Higuain had Rafael Benitez's side ahead at the break.
Florian Thauvin levelled matters but Higuain proved the match winner.
Benitez made four changes to his Napoli side, with the likes of Inler and Dries Mertens coming in as Marek Hamsik dropped to the bench, while Marseille introduced Andre Ayew and Benoit Cheyrou.
Marseille – who entered the match on the back of a six-match winless streak - were nearly behind after just six minutes as Mertens curled just wide when sent through by Jose Callejon, but it was the French side who would take the lead four minutes later.
Andre Ayew was the scorer, rising highest to nod Thauvin's corner past Pepe Reina, and with no player on the far post, Benitez was unhappy with his side's organisation.
The hosts responded strongly though, Mertens forcing Marseille goalkeeper Steve Mandanda into a diving save, before Inler levelled in superb circumstances in the 22nd minute.
A corner – which initially saw Raul Albiol's header well saved – was not properly cleared and fell to Inler who controlled on his chest 20 yards out before lashing a left-footed volley into the bottom-right corner.
And Napoli took the lead just two minutes later when Higuain also thumped a volley past Mandanda.
Callejon crossed for Goran Pandev, his header across the face of goal was not dealt with by defender Souleymane Diawara and the ball fell kindly for the striker who scored with a powerful effort.
Jordan Ayew had a half-chance for Marseille before Higuain poked just wide with five minutes remaining as Napoli finished the first half well.
Marseille improved significantly after the break with Thauvin shooting wide twice, while Dimitri Payet did the same after a mazy run.
Thauvin drew them level in the 64th minute though, stealing in behind Pablo Armero to convert Payet's cross.
Parity lasted just 11 minutes as Higuain scored again, with Mertens' clever cross easily tapped in by the striker at the far post.
Napoli substitute Lorenzo Insigne hit the post with a curling strike, but three goals were enough as they posted their fifth win in a row in all competitions.