The Parisian club has now claimed the prestigious trophy on 14 separate times.
Paris Saint-Germain needed a dramatic equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The Champions League holders seemed to be sailing towards a comfortable win in the match featuring the French league champions and the French Cup winners after the French winger opened the scoring early on.
Yet, Marseille fired two times in the closing moments to seize a surprise advantage. Initially, the English forward scored from the spot-kick, before the defender unfortunately directed 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 final seconds to force the match into a penalty shootout. PSG goalkeeper Chevalier then stood as the key figure, saving crucial attempts from Matt O'Riley and Traore.
In the shootout, Ramos, the midfielder, the full-back, and Desire Doue all scored successfully for Paris Saint-Germain to complete a convincing penalty win.
Now 14-time champions PSG, who met last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now lifted this competition for the 12th time in the past 13 years.