PSG has now secured the prestigious cup on fourteen different times.
The Parisian giants needed 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 Champions League holders seemed to be sailing towards a straightforward triumph in the match featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille fired two times late to seize a shock advantage. First, Mason Greenwood converted from the spot-kick, before the defender unfortunately turned the ball into his own net for an own-goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a crucial equaliser in the dying seconds to send the match into a deciding shootout. PSG goalkeeper Chevalier then emerged as the hero, stopping crucial kicks from O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all scored successfully for Paris Saint-Germain to complete a 4-1 penalty victory.
Now 14-time winners PSG, 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 seasons.