The Parisian club has now claimed the prestigious cup on fourteen separate occasions.
Paris Saint-Germain needed a dramatic equaliser followed by a successful spot-kick decider to overcome their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup victory.
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 scoring in the opening stages.
However, Marseille struck twice in the closing moments to take a shock advantage. First, Mason Greenwood converted from the penalty spot, before Willian Pacho inadvertently turned the ball into his own net for an own goal.
In a breathtaking twist of events, Goncalo Ramos grabbed a vital leveler in the final seconds to send the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, stopping crucial kicks from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted with composure for PSG to complete a 4-1 penalty win.
The record winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now lifted this trophy for the 12th time in the last 13 years.