PSG has now secured the prestigious trophy on 14 different occasions.
Paris Saint-Germain needed a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders seemed to be sailing towards a straightforward win in the showdown featuring the Ligue 1 winners and the Coupe de France holders after Ousmane Dembele opened the scoring early on.
However, Marseille fired twice late to take a shock advantage. Initially, Mason Greenwood scored from the spot-kick, before the defender inadvertently directed the ball into his own net for an own-goal.
In a remarkable turn of events, Goncalo Ramos snatched a vital leveler in the final moments to force the contest into a penalty shootout. The Parisian shot-stopper Chevalier then stood as the key figure, saving crucial kicks from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, the full-back, and the young talent all scored with composure for Paris Saint-Germain to seal a 4-1 shootout victory.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this trophy for the twelfth time in the last thirteen seasons.