Brazilian talisman Neymar was named on the bench from the PSG side that went down to Lorient last Sunday, as Sergio Rico continued in goal ahead of Keylor Navas.
Mauricio Pochettino's side made a bright start nine minutes in when Kylian Mbappe beat one challenge to get on the end of Angel Di Maria's ball for a neat finish past Steve Mandanda.
Di Maria had his evening cut short two minutes later as he walked off the field with a knock to make way for Pablo Sarabia.
The Parisans still bossed proceedings and doubled their lead midway in the first half after Mauro Icardi fortuitously helped a cross from Alessandro Florenzi beyond Mandanda.
It almost got worse for Marseille a minute from the half-hour mark when a first-time strike from Leandro Paredes came off the right-hand post before rolling into touch.
There were no substitutes from any of the two sides as the second half commenced, with Marseille having it all to do in order to salvage something from the clash.
The French however nearly found a lifeline moments from the break through a long-range strike from Florian Thauvin, but he found Rico equal to the task.
Neymar entered from the bench late in the half, with Icardi withdrawn as Paredes made way for Danilo Pereira in a double substitution for the visitors.
There were chances either side late on with Rico parrying a near post attempt from Luis Henrique before Neymar blazed a cutback from Sarabia.
Marseille finished the match with ten players after Dimitri Payet received a straight red card in stoppage time for a rash challenge on Marco Verratti, as the visitors claimed the spoils in Le Classique.