Aubameyang won a penalty which was converted by Mason Greenwood before the Gabon striker doubled Marseille's lead just past the midway point in the first half at the Velodrome.
Newly-promoted Paris FC hit back to draw level with goals by Ilan Kebbal and Moses Simon, only for Aubameyang to restore Marseille's lead before Pierre-Emile Hojbjerg and youngster Robinio Vaz added further goals late on.
Marseille were plunged into crisis last weekend when a fight broke out between star player Adrien Rabiot and English winger Jonathan Rowe in the dressing room at the end of the 1-0 opening-round defeat at Rennes.
France midfielder Rabiot was later put up for sale, while Marseille sought to accelerate plans to move on Rowe after the bust-up which club president Pablo Longoria described as "extremely violent".
"He made a mistake, but I hope there is a chance we can put things back together. I am not going to close the door on anyone," De Zerbi said when asked if he would like Rabiot to stay.
"It is not me who decides, but I am willing to offer my hand to anyone and if I can help in any way to resolve things I am ready to do whatever it takes."
For now, Rabiot is on the market with just over a week of the transfer window left, and last season's Ligue 1 runners-up took to the field without him against the team from the capital.