The Parisian club has now won 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 the Gulf and secure a record-extending fourth consecutive French Super Cup victory.
The European champions seemed to be sailing towards a straightforward triumph in the match featuring the French league winners and the French Cup holders after Ousmane Dembele opened the scoring early on.
However, Marseille fired twice in the closing moments to take a surprise lead. 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, Goncalo Ramos grabbed a vital leveler in the final seconds to force the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, stopping crucial attempts from O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted with composure for PSG to complete a convincing shootout victory.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a league and cup double, have now lifted this trophy for the 12th time in the last thirteen seasons.