The Parisian club has now claimed the season-opening cup on fourteen separate times.
Paris Saint-Germain needed a dramatic leveler followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup victory.
The Champions League holders seemed to be sailing towards a straightforward win in the match featuring the Ligue 1 winners and the Coupe de France winners after the French winger found the scoring in the opening stages.
Yet, Marseille struck two times in the closing moments to take a shock lead. First, the English forward scored from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own-goal.
In a breathtaking turn of events, the Portuguese striker grabbed a vital leveler in the dying moments to force the contest into a penalty shootout. The Parisian shot-stopper Chevalier then stood as the key figure, saving decisive attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored successfully for Paris Saint-Germain to complete a convincing penalty victory.
The record champions 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 12th time in the past thirteen seasons.