PSG has now claimed the prestigious trophy on 14 different times.
The Parisian giants required a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a record-extending fourth consecutive Trophee des Champions victory.
The Champions League holders seemed to be sailing towards a straightforward win in the match between the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the net early on.
However, Marseille fired two times in the closing moments to take a surprise advantage. Initially, the English forward converted from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a breathtaking turn of events, Goncalo Ramos snatched a vital leveler in the dying moments to send the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving decisive attempts from O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, the full-back, and the young talent all converted successfully for Paris Saint-Germain to seal a 4-1 shootout victory.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a league and cup double, have now lifted this competition for the 12th time in the past thirteen years.