The Parisian club has now won the prestigious trophy on 14 different occasions.
Paris Saint-Germain needed a stoppage-time equaliser followed by a successful penalty shootout to overcome their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be sailing towards a straightforward triumph in the showdown between the French league winners and the French Cup holders after the French winger opened the net early on.
However, Marseille struck twice late to seize a surprise advantage. First, the English forward scored from the spot-kick, before the defender unfortunately directed the ball into his own net for an own goal.
In a remarkable turn of fortune, Goncalo Ramos snatched a vital leveler in the final moments to force the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive kicks from O'Riley and Hamed Traore.
From the spot, Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to complete a 4-1 penalty victory.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 runners-up Olympique de Marseille after completing a domestic double, have now won this trophy for the 12th time in the last thirteen years.