The Parisian club has now won the prestigious cup on 14 separate occasions.
Paris Saint-Germain needed a stoppage-time leveler followed by a perfect spot-kick decider to overcome Marseille in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The European champions seemed to be coasting towards a straightforward win in the match between the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele found the scoring in the opening stages.
Yet, Marseille fired twice late to seize a shock advantage. First, Mason Greenwood converted from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own-goal.
In a remarkable twist of events, the Portuguese striker snatched a vital leveler in the dying moments to send the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, stopping crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, the full-back, and Desire Doue all scored with composure for Paris Saint-Germain to seal a 4-1 penalty win.
The record winners PSG, who met last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now won this competition for the twelfth time in the past 13 seasons.