The Parisian club has now won the prestigious cup on 14 separate times.
Paris Saint-Germain required a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be coasting towards a comfortable win in the showdown between the Ligue 1 champions and the Coupe de France winners after Ousmane Dembele found the net in the opening stages.
However, Marseille struck two times in the closing moments to seize a shock lead. First, Mason Greenwood scored from the penalty spot, before the defender unfortunately turned the ball into his own net for an own-goal.
In a remarkable twist of fortune, the Portuguese striker grabbed a crucial equaliser in the final moments to send the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive attempts from O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, the full-back, and Desire Doue all converted successfully for Paris Saint-Germain to complete a convincing shootout win.
Now 14-time winners PSG, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a league and cup double, have now won this competition for the twelfth time in the past 13 seasons.