The Bianconeri controlled the game well but could only muster one goal despite playing a team with just one point to their name.
Federico Bernardeschi's classy cross from the right was one of the few moments of true quality in the final third, which Kean met with a darting run to the near post in the 18th minute.
Malmo rarely threatened in the time that remained, but Juventus never looked like claiming an emphatic win either and their solitary goal proved enough to see them finish above Chelsea, who conceded a 94th-minute equaliser in their 3-3 draw with Zenit.
Kean came close to opening the scoring in the sixth minute after being slipped into the area by Paulo Dybala, but the striker lashed his low effort just wide of the bottom-right corner.
The Italian made amends 12 minutes later, however, nipping in front of Ismael Diarra Diawara to nod Bernardeschi's outstanding outside-of-the-boot cross in and put Juventus ahead.
Kean then laid the ball off to Arthur just inside the box on the stroke of half-time, but the midfielder lost his balance as he took the shot on and fired narrowly past the top-right corner.
Juventus, despite dominating the game and holding the lead, lacked conviction in the final third as Adrien Rabiot burst forward down the left and smashed a shot into the side-netting after the break.
Kean forced a low save in the 66th minute and should have doubled Juventus' advantage with under 10 minutes remaining after Diarra Diawara spilled Rabiot's initial effort, but the goalkeeper recovered to make a stunning save at point-blank range and deny the 21-year-old, whose contribution proved decisive in settling the group thanks to events in St. Petersburg.