PSG has now secured the prestigious cup on 14 separate occasions.
Paris Saint-Germain needed a stoppage-time leveler followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be coasting towards a straightforward triumph in the match between the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the net early on.
Yet, Marseille struck two times in the closing moments to take a surprise lead. Initially, Mason Greenwood scored from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable turn of fortune, Goncalo Ramos grabbed a vital equaliser in the dying seconds to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, stopping decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and the young talent 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 runners-up Marseille after achieving a league and cup double, have now won this trophy for the 12th time in the past thirteen years.