PSG has now claimed the prestigious trophy on 14 separate occasions.
Paris Saint-Germain required a dramatic equaliser followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The European champions appeared to be sailing towards a comfortable win in the showdown between the Ligue 1 winners and the French Cup holders after Ousmane Dembele found the net early on.
However, Marseille struck twice in the closing moments to take a shock advantage. Initially, the English forward converted from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker snatched a vital equaliser in the final moments to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, saving decisive kicks from O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all converted with composure for PSG to seal a 4-1 penalty win.
Now 14-time champions PSG, who faced last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now lifted this competition for the 12th time in the last 13 years.