PSG has now claimed the season-opening trophy on 14 different times.
Paris Saint-Germain required a stoppage-time leveler followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The European champions appeared to be coasting towards a straightforward triumph in the showdown featuring the Ligue 1 winners and the Coupe de France winners after Ousmane Dembele opened the net in the opening stages.
Yet, Marseille fired two times in the closing moments to take a surprise lead. Initially, Mason Greenwood scored from the penalty spot, before Willian Pacho unfortunately directed the ball into his own net for an own goal.
In a breathtaking turn of events, the Portuguese striker snatched a crucial equaliser in the dying moments to send the match into a deciding shootout. PSG goalkeeper Chevalier then emerged as the key figure, stopping decisive attempts from O'Riley and Traore.
From the spot, Ramos, Vitinha, the full-back, and the young talent all scored successfully for PSG to complete a 4-1 penalty victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now won this competition for the twelfth time in the last thirteen seasons.
