PSG has now won the prestigious trophy on 14 separate times.
The Parisian giants required a stoppage-time equaliser followed by a perfect penalty shootout to get past their arch-rivals in Kuwait and secure a fourth straight French Super Cup victory.
The Champions League holders seemed to be sailing towards a comfortable triumph in the showdown featuring the Ligue 1 winners and the French Cup winners after the French winger opened the net early on.
However, Marseille struck twice in the closing moments to take a shock advantage. Initially, the English forward converted from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own-goal.
In a breathtaking twist of fortune, Goncalo Ramos snatched a vital equaliser in the dying moments to send the match into a penalty shootout. PSG goalkeeper Chevalier then stood as the key figure, stopping crucial kicks from O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted with composure for PSG to complete a convincing penalty win.
The record champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after completing a domestic double, have now lifted this trophy for the twelfth time in the past 13 seasons.