PSG has now claimed the prestigious cup on 14 different times.
The Parisian giants required a stoppage-time equaliser followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The European champions appeared to be coasting towards a straightforward win in the match between the Ligue 1 winners and the Coupe de France holders after the French winger found the net in the opening stages.
Yet, Marseille fired twice late to take a surprise lead. First, the English forward converted from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own goal.
In a remarkable turn of events, the Portuguese striker grabbed a crucial equaliser in the final seconds to send the contest into a penalty shootout. The Parisian shot-stopper Chevalier then stood as the hero, saving decisive attempts from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for PSG to seal a convincing penalty win.
The record champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now won this competition for the twelfth time in the last 13 years.