Zlatan, who was made captain for the night, enjoyed a standing ovation from the sell-out home crowd when he was taken off in the 85th minute.
"I got goose bumps. It felt like I was home," Zlatan told TV3 after the game.
The 34-year-old, who had booked the city's main square to show the match on a giant screen for those without tickets, said the whole experience in Malmö was one to remember.
"It was a great moment for me and my family. This is where it all began," said the striker who left Malmö in 2001 to join Ajax.
As a contest, the penultimate match in Group A was over within 15 minutes as Adrien Rabiot and Angel Di Maria put the Parisians 2-0 ahead.
Ibrahimovic scored himself shortly after the break, and when Malmö captain Markus Rosenberg failed to convert a penalty in the 61st minute, Angel Di Maria and Lucas extended the vistors' lead to finish with an emphatic 5-0 scoreline.
PSG go through to the knockout stage as runners-up to Real Madrid, who beat Shakhtar Donetsk 4-3.
Malmö and Shakhtar have three points in a straight fight to finish third to qualify for the Europa League. The Swedes face Real Madrid at the Santiago Bernabeu in their final game while the Ukrainian side meet Zlatan and PSG.