The Parisian club has now claimed the prestigious trophy on 14 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 capture a fourth straight French Super Cup victory.
The European champions appeared to be sailing towards a comfortable triumph in the match featuring the French league champions and the French Cup holders after the French winger opened the scoring early on.
However, Marseille struck two times late to take a surprise lead. First, the English forward converted from the penalty spot, 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 crucial equaliser in the dying moments to send the contest into a penalty shootout. PSG goalkeeper Chevalier then emerged as the key figure, saving decisive kicks from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all converted successfully for Paris Saint-Germain to complete a convincing penalty victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now lifted this competition for the 12th time in the past 13 years.