The Parisian club has now won the season-opening trophy on 14 different times.
The Parisian giants needed 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 seemed to be coasting towards a comfortable win in the showdown featuring the Ligue 1 winners and the French Cup holders after the French winger opened the net early on.
However, Marseille struck twice in the closing moments to seize a surprise advantage. Initially, the English forward converted from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker snatched a crucial leveler in the dying seconds to send the match into a penalty shootout. The Parisian shot-stopper Chevalier then emerged as the hero, saving decisive attempts from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted with composure for Paris Saint-Germain to complete a 4-1 penalty win.
The record champions PSG, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now lifted this competition for the 12th time in the last 13 years.