PSG has now won the prestigious trophy on 14 different times.
Paris Saint-Germain needed a dramatic leveler followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup victory.
The European champions appeared to be coasting towards a comfortable triumph in the match between the French league winners and the Coupe de France holders after the French winger opened the scoring early on.
Yet, Marseille fired two times in the closing moments to take a surprise advantage. First, the English forward converted from the spot-kick, before Willian Pacho unfortunately turned the ball into his own net for an own-goal.
In a breathtaking turn of events, the Portuguese striker snatched a vital equaliser in the dying seconds to send the contest into a deciding shootout. The Parisian shot-stopper Chevalier then emerged as the hero, saving crucial attempts from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, the full-back, and the young talent all scored successfully for Paris Saint-Germain to complete a 4-1 penalty win.
Now 14-time winners PSG, who faced 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 past 13 years.