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."
Marseille interim coach Franck Passi lamented his side's slow start to both halves, rueing a lack of concentration.
"You must not give away goals like the ones we conceded because it's difficult for us to score them," he said. "It needed to stay at 1-1 for longer, we had the chances but we only scored two goals.
"We couldn't to afford to concede a goal so quickly, we needed to be more focused."
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.
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.
Blanc's side were ahead though with their first attack as Angel Di Maria, provider of 18 assists in his first Ligue 1 campaign, delivered another from a wicked right-wing cross that was turned in by Matuidi from close range.
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 Thiago Silva's leg to wrong-foot Sirigu.
Thauvin was fortunate to escape punishment when he blocked Ibrahimovic's goalbound strike with his hand shortly before the interval, but Marseille were caught out seconds after the restart as Nicolas Nkoulou bundled over Matuidi inside the box.
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.
Matuidi then released Ibrahimovic to stroke home a fourth on 82 minutes and guarantee PSG a 10th successive win over Marseille, despite Batshuayi converting a rebound three minutes from the end after Sirigu could only parry Benjamin Mendy's low shot.
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.