The Parisian club has now won the season-opening trophy on fourteen separate times.
Paris Saint-Germain needed a stoppage-time equaliser followed by a perfect spot-kick decider to overcome 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 win in the match between the Ligue 1 winners and the Coupe de France winners after the French winger found the scoring in the opening stages.
However, Marseille fired twice in the closing moments to take a surprise lead. First, Mason Greenwood converted from the penalty spot, before the defender unfortunately directed the ball into his own net for an own goal.
In a remarkable turn of fortune, Goncalo Ramos snatched a crucial equaliser in the final moments to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, stopping crucial kicks from O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for Paris Saint-Germain to complete a convincing penalty win.
The record champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now lifted this competition for the 12th time in the last thirteen seasons.