The Parisian club has now claimed the prestigious trophy on 14 separate occasions.
Paris Saint-Germain needed a dramatic 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 victory.
The European champions appeared to be sailing towards a comfortable win in the match featuring the Ligue 1 winners and the Coupe de France holders after Ousmane Dembele found the net early on.
Yet, Marseille fired twice in the closing moments to seize a surprise lead. Initially, Mason Greenwood scored from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable twist of events, the Portuguese striker grabbed a crucial equaliser in the final moments to send the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, stopping decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all scored successfully for PSG to complete a convincing shootout win.
The record champions Paris Saint-Germain, who faced last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now lifted this trophy for the 12th time in the past 13 years.