PSG has now claimed the prestigious trophy on 14 different times.
The Parisian giants required a dramatic equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and capture a record-extending fourth consecutive Trophee des Champions victory.
The Champions League holders appeared to be coasting towards a straightforward triumph in the match featuring the Ligue 1 winners and the Coupe de France winners after Ousmane Dembele opened the net in the opening stages.
Yet, Marseille struck twice late to seize a shock advantage. First, Mason Greenwood converted from the spot-kick, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of fortune, Goncalo Ramos grabbed a vital equaliser in the final moments to send the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, the full-back, and the young talent all converted with composure for PSG to seal a convincing shootout win.
The record champions Paris Saint-Germain, who faced last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now lifted this competition for the twelfth time in the past thirteen seasons.