PSG has now claimed the prestigious trophy on 14 separate occasions.
The Parisian giants needed a dramatic equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup victory.
The European champions seemed to be sailing towards a straightforward triumph in the showdown featuring the Ligue 1 winners and the French Cup winners after the French winger found the scoring early on.
However, Marseille fired twice in the closing moments to seize a surprise lead. First, Mason Greenwood converted from the penalty spot, 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 equaliser in the dying seconds to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, saving crucial attempts from O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, the full-back, and the young talent all scored with composure for Paris Saint-Germain to complete a 4-1 penalty victory.
The record champions PSG, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now won this competition for the 12th time in the past thirteen seasons.