The Parisian club has now secured the prestigious trophy on fourteen separate times.
Paris Saint-Germain needed a stoppage-time leveler followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The European champions appeared to be coasting towards a comfortable win in the match featuring the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the net early on.
Yet, Marseille fired twice late to take a shock advantage. Initially, the English forward converted from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own-goal.
In a remarkable turn of fortune, Goncalo Ramos snatched a crucial equaliser in the final seconds to force the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, saving decisive attempts from O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted with composure for PSG to seal a convincing penalty win.
The record winners PSG, who met last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now won this competition for the 12th time in the last 13 years.
