Goals from Koke and Raul Garcia put Malmo to the sword and helped Atletico Madrid towards the next stage of the Champions League.
Koke netted part-way through the first half from a Juanfran cross and Garcia found the target late in the second when the hosts failed to clear a cross.
Malmo had previously recorded clean sheets in their home Champions League games this season and gave Atletico a tough game, calling Miguel Angel Moya into action repeatedly and hitting the post with the score at 1-0.
The victory means Atletico have nine points from their four games while Juventus’ dramatic 3-2 win over Olympiacos has the Italians and the Greeks level on six points.
Malmo 0-2 Atletico
Koke 30, Garcia 78
Malmo: Olsen; Tinnerholm, Johansson, Halsto, Helander, Ricardinho; Eriksson, Adu, Fosberg; Thelin, Rosenberg
Malmo substitutes: Azinovic, Concha, Konate, Thern, Kroon, Rakip, Mehmeti
Atletico Madrid: Moya; Juanfran, Miranda, Godin, Siqueira; Arda, Mario, Gabi, Koke; Raul Garcia, Mandzukic
Atletico substitutes: Oblak, Gamez, Gimenez, Tiago, Griezmann, Rodriguez, Cerci
Referee: Mark Clattenburg