The Spanish champions prevailed on a tough night thanks to Koke's neat flick on the half hour and Raul Garcia's emphatic finish 12 minutes from time.
But before the second goal, Simeone's men were given a stern examination by the Swedish champions, who saw Anton Tinnerholm's goalbound volley cleared by Diego Godin, and Markus Rosenberg rattled the post with a ferocious shot as Malmo laid siege to the Atletico goal in the second half.
The result leaves Atletico on nine points with two games to go, but Simeone was glad to get maximum points on a difficult night for his side.
He said: "We played a great game against a great opponent. We knew they'd be brave at home, with the young players in the team, and it’s a hard and difficult place to come. We had to have a great game.
"We knew the game would be like this, because Malmo have given a good showing in the games they've played so far, except the second half at the [Vicente] Calderon.
"We knew how we had to play. We suffered a lot for 15 or 20 minutes in the second half until the goal by Garcia."
Despite being three points clear at the top of Group A with two games to play thanks to a fifth consecutive win in all competitions, Simeone is taking nothing for granted.
"The standings are an unusual situation and I don't think positively because there are many possibilities," Simeone told AS.
"We're dependant on the next match [against Olympiacos] at Vicente Calderon."
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