The Parisian club has now secured the prestigious cup on 14 separate times.
The Parisian giants required a dramatic equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in Kuwait and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be sailing towards a comfortable triumph in the showdown featuring the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the scoring in the opening stages.
Yet, Marseille fired twice late to seize a shock lead. Initially, the English forward scored from the penalty spot, before the defender unfortunately turned the ball into his own net for an own-goal.
In a breathtaking twist of fortune, Goncalo Ramos snatched a vital leveler in the dying seconds to force the match into a deciding shootout. The Parisian shot-stopper Chevalier then emerged as the hero, saving decisive attempts from O'Riley and Traore.
In the shootout, Ramos, Vitinha, the full-back, and Desire Doue all converted successfully for PSG to complete a convincing penalty win.
The record winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now won this trophy for the twelfth time in the last 13 seasons.