The hosts had plenty of the match in Sweden, but could not find a way past the away side's stern defence.
Here, Sports Mole dissects the 90 minutes of action between the two European rivals.
On target: 5
On target: 4
Was the result fair?
In short, no. Malmo deserved to take something from this match, but in the end, they were beaten by a very professional performance. There was not much to separate the two teams in the first period, but Koke's strike on the 30-minute mark ensured that the visitors entered the interval with a one-goal lead. Malmo completely dominated the opening 10 minutes of the second half - hitting the post and creating a number of strong opportunities, but they just could not find the back of the net. The match was more even as the half advanced, but it was Atletico that struck the killer blow 12 minutes from time. Atletico's defensive performance certainly deserved to secure something from the match, but Malmo will be aggrieved that they have been beaten.
The Swedish side entered this match with a very strong home record and it is not difficult to see why that is the case. The home side's supporters were excellent and remained noisy throughout, even when Atletico had secured all the points with a second goal. Malmo began the match on the front foot this evening and will feel that their start should have been rewarded with a goal. Atletico have been around the block a few times, however, and soaked up the pressure before finding a goal of their own. Statistics rarely paint a false picture in football and the fact that Malmo had 18 attempts to Atletico's nine tells the story. Markus Rosenberg and Isaac Kiese Thelin were both excellent in attack, while they provided a threat in wide areas throughout the entirety of the match. Football at this level can be cruel, however, and now they face a huge fight if they are to qualify for the next round.
In many ways, this was a typical Atletico performance. It was not particularly pretty, but it did not need to be. The Spanish champions are perhaps the best team in world football at defending a lead and they were put under serious pressure this evening. Diego Godin and Miranda were both brilliant at the heart of the back four, however, while Koke had a fine night in midfield. It was a strong and professional performance from the visitors rather than an impressive one, but displays of this ilk are an indication of why they have been so successful over the last couple of seasons. If they continue to produce team performances of this level, then they will have a strong chance of making another final. Diego Simeone's side now top Group A on nine points, with Olympiacos second on six and Juventus also on six in third position.
Sports Mole's man of the match
Juanfran: This is not a difficult decision. The Atletico full-back was key to the club's success last season and he has started the new campaign in the same fashion. Malmo just could not come to terms with the defender's runs from deep, while the Spaniard set up both of his side's goals this evening with low crosses from the right. The right-back picked up a yellow early in the second period, but it did not harm his overall performance.
This one is perhaps slightly harsh, but it goes to Malmo skipper Rosenberg. The striker hit a tame free kick into the Atletico wall early in the second period, but the ball dropped straight back to his feet. Atletico goalkeeper Miguel Moya was stranded after diving the other way, but Rosenberg could only rattle the post. It was far from an easy chance, but one that should have been taken.
English referee Mark Clattenburg had a busy night in Sweden. The first period saw the official produce just one yellow card, but he booked three of Atletico's back four in the opening eight minutes of the second half. In total, Clattenburg got his card out on seven occasions, which is an indication of the feistiness between the two sides. Overall, however, neither manager would have had any complaints about the official's performance.
Malmo: Malmo have the small matter of the final of the Swedish Super Cup on Sunday, with Elfsborg their opponents.
Atletico: The capital outfit return to La Liga action on Sunday evening with a trip to struggling Basque side Real Sociedad.