Blaise Matuidi struck PSG's opening goal inside two minutes at the Stade de France, but Marseille hit back just 10 minutes later through on-loan Newcastle midfielder Florian Thauvin.
Ibrahimovic then converted a penalty immediately after half-time to restore the capital club's lead, before he played in Edinson Cavani to add a third goal on 56 minutes.
The 34-year-old Swedish star signed off in trademark spectacular style with his second of the evening, the 156th and final goal of his PSG career, eight minutes from time as Laurent Blanc's side repeated last year's domestic treble despite a late consolation from Michy Batshuayi.
“I'm very happy to win my final match with a fantastic team,” said Ibrahimovic.
“We've worked hard over the four years. It was an incredible adventure for me, especially when you know how things were when I arrived and how they are now. It's mission accomplished. I didn't learn to speak French but I've won everything. I came, I saw, I conquered.”
With the Ligue 1 crown and French League Cup already in the bag, PSG were aiming to move level with record 10-time French Cup winners Marseille in a repeat of the 2006 final, won 2-1 by Paris.
Ibrahimovic, who last weekend broke Argentine striker Carlos Bianchi's single-season club record of 37 league goals, was aiming to bring down the curtain the down on a glittering four-year stay in the French capital in fitting fashion having already helped PSG to 11 trophies.
PSG manager, Laurent Blanc, later withdrew Ibrahimovic, who will leave Paris when his contract expires at the end of June, to a rapturous ovation late on in the final act of a remarkable chapter in PSG's history.