PSG has now won the prestigious trophy on 14 separate times.
Paris Saint-Germain required a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The Champions League holders seemed to be sailing towards a comfortable triumph in the match featuring the French league champions and the French Cup holders after Ousmane Dembele opened the scoring early on.
However, Marseille fired twice in the closing moments to seize a shock advantage. Initially, the English forward converted from the penalty spot, before Willian Pacho unfortunately directed the ball into his own net for an own goal.
In a breathtaking turn of fortune, the Portuguese striker grabbed a crucial leveler in the dying seconds to force the match into a deciding shootout. The Parisian shot-stopper Chevalier then emerged as the hero, saving decisive attempts from O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted with composure for Paris Saint-Germain to complete a 4-1 shootout victory.
The record champions PSG, who faced last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now lifted this competition for the 12th time in the past 13 years.
