The Parisian club has now won the season-opening cup on fourteen different occasions.
Paris Saint-Germain needed a dramatic leveler followed by a perfect penalty shootout to get past their arch-rivals in Kuwait and capture a fourth straight French Super Cup title.
The European champions seemed to be coasting towards a comfortable triumph in the match featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the scoring in the opening stages.
Yet, Marseille struck twice in the closing moments to seize a shock advantage. First, Mason Greenwood scored from the spot-kick, before the defender inadvertently turned the ball into his own net for an own-goal.
In a breathtaking turn of fortune, Goncalo Ramos grabbed a vital leveler in the dying moments to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving crucial attempts from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and the young talent all converted successfully for Paris Saint-Germain to complete a 4-1 shootout win.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after completing a league and cup double, have now won this competition for the twelfth time in the last 13 years.