The Parisian club has now secured the season-opening cup on 14 separate occasions.
Paris Saint-Germain needed a stoppage-time leveler followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and secure a fourth straight French Super Cup title.
The Champions League holders appeared to be coasting towards a straightforward win in the match between the Ligue 1 winners and the French Cup winners after Ousmane Dembele opened the net early on.
However, Marseille fired twice in the closing moments to take a shock 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 events, Goncalo Ramos grabbed a crucial equaliser in the final seconds to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, stopping decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored successfully for Paris Saint-Germain to seal a 4-1 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 trophy for the twelfth time in the last 13 years.
