The Parisian club has now secured the season-opening cup on 14 separate occasions.
Paris Saint-Germain required a dramatic leveler followed by a successful penalty shootout to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be sailing towards a comfortable win in the showdown featuring the French league champions and the French Cup winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille fired twice in the closing moments to seize a shock lead. First, the English forward converted from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable twist of fortune, Goncalo Ramos grabbed a vital equaliser in the final seconds to force the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, stopping decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to seal a 4-1 penalty win.
The record champions PSG, who met last season's Ligue 1 runners-up Marseille after completing a domestic double, have now won this trophy for the 12th time in the last 13 years.