PSG has now won the season-opening cup on 14 separate times.
Paris Saint-Germain required a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be coasting towards a straightforward win in the showdown featuring the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the scoring early on.
However, Marseille fired twice in the closing moments to take a shock advantage. Initially, Mason Greenwood converted from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own goal.
In a remarkable turn of events, the Portuguese striker snatched a vital leveler in the final moments to send the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving crucial attempts from O'Riley and Traore.
In the shootout, Ramos, Vitinha, the full-back, and the young talent all scored successfully for Paris Saint-Germain to seal a 4-1 penalty victory.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now won this trophy for the 12th time in the past thirteen years.