The Parisian club has now claimed the season-opening cup on fourteen different occasions.
Paris Saint-Germain required a stoppage-time equaliser followed by a perfect spot-kick decider to get past Marseille in the Gulf and capture a fourth straight French Super Cup victory.
The Champions League holders seemed to be coasting towards a comfortable win in the match between the Ligue 1 winners and the Coupe de France holders after Ousmane Dembele found the net early on.
However, the southern French side struck twice late to seize a surprise lead. First, the English forward scored from the penalty spot, before Willian Pacho inadvertently turned the ball into his own net for an own-goal.
In a remarkable twist of events, Goncalo Ramos grabbed a vital 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 Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all scored successfully for PSG to seal a convincing penalty win.
Now 14-time 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 last 13 seasons.
