The Parisian club has now secured the prestigious cup on 14 separate times.
Paris Saint-Germain needed a dramatic leveler followed by a successful penalty shootout to overcome their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be coasting towards a straightforward triumph in the match featuring the French league winners and the Coupe de France holders after the French winger opened the scoring in the opening stages.
However, Marseille fired two times late to seize a surprise lead. First, Mason Greenwood converted from the spot-kick, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a breathtaking twist of events, the Portuguese striker snatched a crucial leveler in the dying seconds to send the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving crucial kicks from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all converted with composure for PSG to seal a 4-1 penalty victory.
Now 14-time winners PSG, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now won this competition for the twelfth time in the last 13 years.