It took last year’s finalists until after half-time to make the breakthrough, but once Koke had finished off a fine team move to open the scoring there was little doubt Diego Simeone’s men were headed for victory.
Two goals in two minutes from Mario Mandzukic — his 19th in 23 Champions League appearances — and Antoine Griezmann just after the hour mark made the game safe before late goals from Diego Godin and Alessio Cerci rounded off the scoring.
“We kept going. In the first-half you could see the team was close to the goal, we had some great chances,” said Simeone.
“In the second-half the only difference was the finishing in the final third.”
A second consecutive win for Atletico moves them to the top of Group A alongside Olympiakos on six points after the Greeks beat Juventus 1-0.
Juventus and Malmo are three points further back, but Simeone is still wary of the threat posed by the Italian champions.
“It is complicated and we need to be attentive until the final game.
“Juventus still have two home games to come, so we need to be very careful. Nothing is decided yet.”
Malmo boss Age Hareide, meanwhile, admitted his side had simply been outclassed in the second-half.
“We played well in the first-half, but we lost our way in the second.
“We lacked the same energy in the second-half. We need to analyse the game and learn from it for the return game at home.”
Malmo are making their first appearance in the Champions League group stages, but they withstood an early Atletico onslaught of corners well, whilst Miguel Angel Moya had to turn behind Ricardinho’s free-kick at the other end.
The Spanish champions increased the pressure as the half went on and were somehow denied 10 minutes before the break as Griezmann smashed a shot off the underside of the bar and Erik Johansson cleared Mandzukic’s follow-up effort off the line.
Arda Turan then flashed a shot just wide as Malmo clung on to go in level at the break.
However, their resistance was broken three minutes after the restart as Turan played in Koke and the Spanish international placed the ball into the far corner for his second goal of the season.
Mario Suarez hadn’t scored for two years until finding the target in Atletico’s 2-0 win over Espanyol on Sunday and he nearly had another goal moments later as Robin Olsen flew to his right to make a fine save from the midfielder’s low effort.
Malmo’s only chance to get back into the game came just before the hour mark when Emil Fosberg fired just wide at the end of a promising counter-attack.
Two minutes later it was 2-0 as Koke turned provider with a low cross from the right that Mandzukic bundled home at the near post.
Griezmann then made it three in somewhat fortuitous circumstances as his shot looped up off the legs of Olsen and Mandzukic unselfishly let the ball float into the net to allow the French international to score his first goal at the Calderon as an Atletico player.
A brilliant one-handed save from Olsen prevented Suarez again three minutes from time.
However, the ‘keeper’s good work was undone from the resulting corner as Godin bulleted a header home for the fourth.
And a fine evening for Atletico was rounded off in stoppage time when substitute Cerci curled home his first goal for the club.