PSG has now secured the season-opening trophy on fourteen different times.
Paris Saint-Germain required a stoppage-time equaliser followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The European champions seemed to be sailing towards a comfortable triumph in the match between the Ligue 1 winners and the Coupe de France holders after Ousmane Dembele found the net in the opening stages.
However, Marseille struck two times late to seize a surprise advantage. First, the English forward scored from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of fortune, Goncalo Ramos grabbed a vital leveler in the final moments to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all scored successfully for PSG to complete a convincing penalty win.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now lifted this competition for the twelfth time in the last thirteen seasons.