Thomas Tuchel’s side brushed aside the Swedish minnows at Stamford Bridge thanks to Jorginho’s penalty brace and goals from Andreas Christensen and Kai Havertz.
But Chelsea’s second Group H victory, after losing to Juventus in their previous match, was significantly tarnished by the injuries to Belgium striker Lukaku and Germany forward Werner.
Both had to come off in the first half and Chelsea boss Tuchel will be waiting nervously for an update on their condition.
It would be a major blow if the pair are sidelined for a long period in the midst of a hectic schedule as Chelsea try to retain their position at the top of the Premier League, while pushing to qualify for the Champions League last 16.
Tuchel admitted this week that Lukaku has suffered from mental and physical fatigue amid a draining schedule for club and country.
The Belgium striker has now gone seven Chelsea games without a goal after starting with four in four following his £98 million club record move from Inter Milan.
Frustratingly for Lukaku, he had looked closer to his best and it was his powerful surge that won the penalty converted by Jorginho, in the process causing his injury.
While Werner has endured another difficult season, his injury will leave Havertz as Tuchel’s only experienced option for the central striker’s role.
The decision to allow Tammy Abraham and Olivier Giroud to leave Chelsea since the end of last season might now prove costly for Chelsea.
A relatively undemanding fixture list in the next few weeks is the only saving grace for Tuchel if he is denied the services of Lukaku and Werner for long.
Tuchel said Chelsea were lacking “a little bit of form and enthusiasm” recently after they needed a superb display from Senegal keeper Edouard Mendy to cling onto the win at Brentford on Saturday.
There were no problems in that department as they dominated Malmo from start to finish.
Lukaku went close with a shot from the edge of the area that took a hefty deflection off Eric Larsson, forcing an agile tip over from Johan Dahlin.
Quicker in thought and deed than Malmo, it took just nine minutes for Chelsea to go ahead.
Thiago Silva curled a cross into the Malmo area and Christensen timed his run to meet it with a volley that bounced off the slick turf as it sped past Dahlin from 10 yards.
It was the Denmark defender’s first goal for Chelsea since his debut in 2014.
In the 21st minute, Lukaku bulled his way through the Malmo defence with a twisting run, prompting Lasse Nielsen to haul him down with a crude foul.
Jorginho took the penalty and altered his usual hop-step technique to drive a powerful strike past Dahlin for his first goal this season.
The goal came with collateral damage for Chelsea as Lukaku limped off after lengthy treatment.
Tuchel’s injury woes mounted just before half-time when Werner was forced off after pulling up while turning in the Malmo area.
Havertz provided a welcome glimpse of his quality in his audition for the striker’s role as he bagged Chelsea’s third goal in the 48th minute.
Callum Hudson-Odoi, on for Werner, led a dynamic break that finished with Havertz clipping a composed shot in off the far post.
Chelsea were rampant and Antonio Rudiger’s muscular burst was curtailed by Larsson’s foul, conceding a penalty that Jorginho nonchalantly slotted home in the 57th minute.
The second-placed Blues remain three points behind group leaders Juventus with three games to play.