The Parisian club has now claimed the season-opening cup on fourteen different times.
Paris Saint-Germain needed a dramatic equaliser followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be coasting towards a comfortable win in the showdown between the French league champions and the French Cup winners after Ousmane Dembele opened the scoring early on.
However, Marseille struck two times late to seize a surprise advantage. First, Mason Greenwood scored from the penalty spot, before the defender unfortunately turned the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker snatched a vital equaliser in the dying moments to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving decisive attempts from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, Nuno Mendes, and the young talent all converted successfully for Paris Saint-Germain to complete a convincing shootout win.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now won this competition for the 12th time in the past 13 years.