The Parisian club has now secured the prestigious 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 the Gulf and secure a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be sailing towards a comfortable triumph in the match between the Ligue 1 champions and the Coupe de France holders after the French winger found the net early on.
Yet, Marseille struck twice late to take a surprise advantage. First, the English forward converted from the spot-kick, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of events, the Portuguese striker snatched a vital equaliser in the dying seconds to force 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 Traore.
In the shootout, Goncalo Ramos, the midfielder, Nuno Mendes, and the young talent all converted successfully for PSG to seal a 4-1 penalty victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this competition for the 12th time in the last 13 years.