PSG has now secured the prestigious cup on 14 different times.
Paris Saint-Germain needed a stoppage-time equaliser followed by a perfect spot-kick decider to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be sailing towards a straightforward triumph in the match featuring the French league champions and the French Cup winners after the French winger found the net in the opening stages.
Yet, Marseille struck twice late to take a surprise lead. Initially, Mason Greenwood converted from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a remarkable twist of fortune, Goncalo Ramos grabbed a vital leveler in the dying seconds to send the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving decisive attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted successfully for PSG to seal a convincing shootout victory.
The record champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a domestic double, have now lifted this competition for the twelfth time in the last thirteen years.