The Swedish champions were under pressure to deliver a win, but on the ropes after Gustav Engvall had put the visitors 2-1 up in the 65th minute.
Malmo responded through former Cardiff man Jo Inge Berget, who equalised 10 minutes later.
Then, in the 86th minute, Peruvian Yoshimar Yotun stepped up to be the hero by collecting possession from around 30 yards before unleashing a piledriver off the post and into the top left corner.
Not even the 6ft 7in former Manchester City goalkeeper Andreas Isaksson could get a glove to it. (Mind you, with that swerve you can hardly blame him.)
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