PSG has now secured the prestigious trophy on fourteen separate times.
The Parisian giants needed a stoppage-time equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The European champions appeared to be sailing towards a comfortable win in the match featuring the Ligue 1 champions and the French Cup winners after Ousmane Dembele found the net in the opening stages.
Yet, Marseille struck twice late to seize a shock lead. First, the English forward converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable twist of fortune, the Portuguese striker grabbed a crucial leveler in the final seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving crucial attempts from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, the full-back, and Desire Doue all converted with composure for Paris Saint-Germain to complete a convincing penalty victory.
Now 14-time winners PSG, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now lifted this trophy for the 12th time in the past thirteen years.