The Parisian club has now secured the season-opening trophy on 14 different times.
The Parisian giants required a dramatic equaliser followed by a successful penalty shootout to get past their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The European champions appeared to be coasting towards a straightforward triumph in the showdown featuring the Ligue 1 champions and the Coupe de France winners after Ousmane Dembele found the net early on.
However, Marseille struck two times in the closing moments to take a shock lead. First, Mason Greenwood scored from the penalty spot, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable turn of fortune, Goncalo Ramos snatched a vital leveler in the final moments to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored successfully for Paris Saint-Germain to seal a 4-1 penalty victory.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now won this trophy for the 12th time in the past thirteen years.