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.
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 having already helped PSG to 11 trophies.
However, Abdelaziz Barrada fired an early warning signal to PSG in their quest for another title when the midfielder's 25-yard drive flashed just wide of Salvatore Sirigu's right-hand post with less than a minute gone.
But Marseille, who were hoping to salvage their season after finishing 13th in the league, responded on 12 minutes as Thauvin's strike from just outside the area clipped's Thiago Silva leg to wrong-foot Sirigu.
Ibrahimovic slotted past Steve Mandanda from the penalty spot to put PSG back in front on 47 minutes, before Paris' record goalscorer played in Cavani to steer home a third nine minutes later after Chile international Mauricio Isla lost possession in midfield.
Blanc then 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.
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