PSG has now won the prestigious trophy on 14 different times.
The Parisian giants required a stoppage-time leveler followed by a successful penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The European champions appeared to be coasting towards a straightforward triumph in the match between the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele found the net early on.
However, Marseille struck two times in the closing moments to take a shock advantage. First, the English forward converted from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own-goal.
In a breathtaking turn of fortune, the Portuguese striker grabbed a crucial equaliser in the dying seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, stopping decisive kicks from O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all converted successfully for PSG to complete a 4-1 shootout victory.
Now 14-time champions PSG, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now lifted this competition for the 12th time in the past thirteen years.