PSG has now claimed the season-opening cup on fourteen separate occasions.
Paris Saint-Germain needed a stoppage-time leveler followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be coasting towards a comfortable triumph in the match between the Ligue 1 champions and the French Cup winners after Ousmane Dembele opened the net early on.
Yet, Marseille struck twice in the closing moments to take a shock advantage. First, the English forward converted from the spot-kick, before the defender unfortunately turned the ball into his own net for an own-goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a crucial leveler in the dying seconds to force the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, saving crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, the full-back, and Desire Doue all converted with composure for Paris Saint-Germain to complete a convincing penalty win.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this trophy for the 12th time in the last 13 seasons.