PSG has now claimed the prestigious trophy on fourteen separate times.
The Parisian giants needed a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup victory.
The European champions appeared to be sailing towards a straightforward triumph in the match featuring the Ligue 1 winners and the Coupe de France winners after Ousmane Dembele opened the scoring in the opening stages.
Yet, Marseille fired twice in the closing moments to seize a shock advantage. Initially, the English forward scored from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a breathtaking turn of events, Goncalo Ramos grabbed a vital leveler in the final seconds to force the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving crucial kicks from Matt O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to seal a convincing shootout victory.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now lifted this trophy for the 12th time in the past thirteen years.
