PSG has now won the season-opening cup on 14 different times.
The Parisian giants needed a stoppage-time equaliser followed by a perfect spot-kick decider to get past Marseille in Kuwait and secure a record-extending fourth consecutive French Super Cup victory.
The European champions seemed to be coasting towards a comfortable triumph in the showdown featuring the French league champions and the Coupe de France winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille fired twice in the closing moments to seize a surprise 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, Goncalo Ramos grabbed a crucial equaliser in the final seconds to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to seal a 4-1 penalty win.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now won this competition for the 12th time in the last 13 seasons.