The holders lost their last game against Juventus in Turin but there was no mistake here as the Swedes were completely outclassed.
Andreas Christensen put Chelsea ahead early on with his first goal in 137 appearances for the club from Thiago Silva’s pass and Jorginho doubled the lead from the spot after Lukaku was fouled by Lasse Nielsen, the forward limping off with what looked like an ankle injury.
Werner pulled up with hamstring trouble before half-time, but Chelsea’s progress continued smoothly as his replacement Callum Hudson-Odoi set up another substitute Kai Havertz for a neat finish for their third just after the break.
Malmo were over-powered and Jorginho scored from the spot again after 57 minutes following Eric Larsson’s foul on Antonio Rudiger, with replacement keeper Ismael Diawara having no more success than Johan Dahlin did in the opening half.
This was the most comfortable of nights for Chelsea as they put the misery of their loss to Juventus behind them in emphatic fashion.
The Italians remain three points ahead of Chelsea in Group H, but still have to visit Stamford Bridge.
The Blues were in a different class to their Swedish opponents and effectively settled matters in the 48th minute when Havertz chipped home a composed third goal.
Manager Thomas Tuchel will be highly satisfied with how Chelsea handled this straightforward task against Malmo in a professional and ruthless manner.
They remained in control throughout with their outstanding passing and efficient movement of the ball.
The win, however, was overshadowed by those injuries to Lukaku and Werner.
Lukaku was hurt as he was brought down by Nielsen for Jorginho’s first penalty, seemingly taking the full weight of the Malmo player on his ankle.
The club’s record signing required lengthy treatment and despite walking to the halfway line in an attempt to carry on, he was clearly struggling and substituted.
Werner clutched his hamstring racing into the area and, again, was taken straight off.
Chelsea’s next game is at home to the Premier League’s bottom club Norwich City at Stamford Bridge on Saturday, and Tuchel confirmed Lukaku and Werner will be out for “some matches”.
He must now hope this impressive victory does not come at too much of a cost to his side.