PSG has now secured the prestigious cup on 14 separate times.
The Parisian giants required a dramatic equaliser followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The European champions appeared to be sailing towards a comfortable win in the showdown between the Ligue 1 champions and the French Cup winners after Ousmane Dembele opened the net in the opening stages.
Yet, Marseille fired twice late to take a surprise advantage. Initially, the English forward converted from the penalty spot, before the defender unfortunately directed the ball into his own net for an own-goal.
In a remarkable twist of fortune, the Portuguese striker snatched a crucial leveler in the final moments to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, stopping decisive attempts from Matt O'Riley and Hamed Traore.
From the spot, Ramos, the midfielder, the full-back, and Desire Doue all converted successfully for Paris Saint-Germain to seal a 4-1 shootout victory.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now lifted this competition for the 12th time in the last thirteen years.