PSG has now won the prestigious cup on fourteen separate times.
The Parisian giants needed a stoppage-time equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be sailing towards a comfortable win in the showdown featuring the Ligue 1 winners and the French Cup winners after the French winger opened the net early on.
However, Marseille struck two times in the closing moments to take a shock lead. 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 breathtaking turn of events, the Portuguese striker grabbed a vital equaliser in the dying seconds to force the contest into a deciding shootout. The Parisian shot-stopper Chevalier then stood as the hero, saving decisive kicks from Matt O'Riley and Traore.
From the spot, Ramos, Vitinha, the full-back, and Desire Doue all scored successfully for PSG to seal a 4-1 penalty win.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now won this trophy for the 12th time in the last 13 years.