PSG has now secured the prestigious cup on 14 separate occasions.
The Parisian giants required a stoppage-time leveler followed by a perfect spot-kick decider to get past Marseille in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders appeared to be coasting towards a straightforward win in the match featuring the Ligue 1 champions and the French Cup winners after Ousmane Dembele found the net early on.
Yet, Marseille struck two times in the closing moments to take a surprise advantage. First, the English forward scored from the spot-kick, before Willian Pacho unfortunately turned the ball into his own net for an own-goal.
In a remarkable turn of fortune, Goncalo Ramos snatched a crucial equaliser in the dying moments to send the contest into a penalty shootout. PSG goalkeeper Chevalier then emerged as the key figure, saving decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted successfully for PSG to complete a convincing shootout victory.
The record winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now won this competition for the twelfth time in the last 13 seasons.