The Spanish champions went ahead on the half hour through Koke's neat flick and sealed the points 12 minutes from time courtesy of Raul Garcia's emphatic finish.
But between those goals, last season's losing finalists were given a stern examination by their Swedish counterparts in a frenetic second half.
Diego Godin blocked Anton Tinnerholm's goal-bound volley before Markus Rosenberg's ferocious shot cannoned back off the post as the visitors wobbled.
It took Garcia's drilled finish from inside the box to give Atletico breathing space, making it five wins on the bounce in all competitions as the away side became the first team in eight European outings to win at Malmo.
Despite his two goals to break his La Liga duck against Cordoba at the weekend, Antoine Griezmann was dropped to the bench by Atletico coach Simeone – the Frenchman making way for Garcia.
Malmo goalkeeper Robin Olsen was substituted with a leg injury in the Allsvenskan fixture against Atvidaberg at the weekend and was given an early test when Gabi's in-swinging free-kick glanced off Erik Johansson after three minutes – the shot-stopper doing well to tip the ball wide.
The visitors should have taken the lead after 19 minutes when a slick passing move opened up the Malmo defence and Koke cleverly squared for Garcia 10 yards out, but Olsen made a fine low save.
They were ahead 11 minutes later, though, when another brilliant team move saw Juanfran released down the right and his low cross was beautifully flicked in by Koke from six yards out.
That goal made it six that the midfielder has been involved in during this year's competition.
The Swedish champions put in a spirited showing in the first half, and Isaac Kiese Thelin's powerful header flew wide after 37 minutes.
They ought to have equalised a minute before half-time on the counter as Rosenberg's superb pass found Emil Forsberg, but a heavy first touch allowed Atletico to clear.
Malmo came out fighting after the interval and went agonisingly close to levelling after 48 minutes when Tinnerholm's terrific volley was superbly blocked by Godin.
The visitors went even closer shortly after when Rosenberg reacted quickest to his blocked free-kick to lash a fierce effort against the post.
Atletico were rattled and Guilherme Siqueira's causal chest back to Miguel Angel Moya in the 57th minute afforded Tinnerholm a sight of goal, but the goalkeeper smothered the shot.
Simeone's side weathered the storm before confirming the win in the 78th minute when Juanfran's cross was only half cleared and Garcia arrowed a precise strike into the bottom-left corner, leaving Atletico still leading the way in Group A.
