First-half goals from Adrien Rabiot and Angel Di Maria put the French champions in control before Ibrahimovic struck just after the interval.
Di Maria was then on target again before Lucas added a late fifth to ensure PSG's progression to the knockout phase for the fourth straight year.
“I lived a dream tonight, coming back. On top of that I scored one. I'm very happy,” said Ibrahimovic.
“Since the beginning, there's a great relationship between Malmö's fans and me.”
Fellow goalscorer Rabiot added: “We thought it would have been harder. We did the job and we're through. I'm very proud of my first Champions League goal.”
However, Real Madrid's 4-3 victory over Shakhtar Donetsk means that PSG go through as runners-up, exposing Laurent Blanc's side to the possibility of being drawn against Barcelona or Bayern Munich in the next round.
“There was a chance to finish top of our group. It was a shame we had that defeat (against Real),” bemoaned Blanc, whose side round out their group campaign at home to Shakhtar.
Malmö can still drop into the Europa League but the odds are stacked against them with the Swedes needing to pick up at least a point at the Santiago Bernabeu in a fortnight to stand a chance.
Zlatan Ibrahimovic leaving the pitch. Photo: Andreas Hillergren/TT
Much was made of Ibrahimovic returning to the club with whom his professional career began 16 years ago, with the Sweden captain booking out Malmö's main square to show the match on a big screen for those without tickets.
The 34-year-old was also handed the PSG captain's armband for the occasion, but there was little room for sentiment once the game kicked off as the visitors silenced the home fans just three minutes in when Rabiot headed home a Gregory van der Wiel cross for his first European goal.
PSG were cruising with less than a quarter-hour gone as Di Maria doubled their lead, curling low just inside Johan Wiland's right-hand post after he was picked out on the edge of the area by Blaise Matuidi.
Norway forward Jo Inge Berget came close to pulling one back, jinking past Van der Wiel after linking up with Markus Rosenberg only to be denied by a fine stop from PSG goalkeeper Kevin Trapp.
Malmö fans watching the game on a big screen TV. Photo: Jon Willén/TT
Ibrahimovic then took centre stage five minutes into the second half, beating Wiland from a tight angle to end an 11-month European goal drought and erase any hopes of a Malmö fightback.
The hosts were awarded a penalty on 61 minutes after Nikola Djurdjic was fouled by Maxwell, but Rosenberg smacked his spot-kick against the post.
Di Maria notched his second of the evening soon after as Maxwell atoned for his earlier error by finding the unmarked Argentine who headed past a helpless Wiland.
That was Di Maria's last act as he was immediately replaced by Lucas and it was the Brazilian who capped the rout by curling home a free-kick eight minutes from time.
The sell-out crowd at the Malmö New Stadium then rose in unison to applaud their hero as Ibrahimovic made way for Jean-Kevin Augustin late on.