After weathering an early storm from the Swedish side, the Blues began to turn the screw but struggled to find a breakthrough.
But a rare moment of brilliance came ten minutes after the break when N'Golo Kante started a quick move, finished by Olivier Giroud.
Ross Barkley made it 2-0 when he curled in a stunning free-kick from close range before Callum Hudson-Odoi found the bottom corner to seal the win.
But with tonight's game the final audition for players wanting to start in the Carabao Cup final on Sunday, some will not have done themselves any favours.
Willy Caballero
Although Malmo started strongly, the goalkeeper was rarely troubled between the sticks.
Cesar Azpilicueta
Almost gave the Blues an inadvertent lead when sliding in at the near post but his effort bounced off him and into the hands of a very grateful Johan Dahlin.
Not troubled at the back and rested for final minutes to get him in top condition to face Raheem Sterling, Leroy Sane & Co.
Antonio Rudiger
Got beaten by the turn when Markus Rosenborg flashed wide but other than that had a gentle evening.
The pitch invader who ran across the field just after half-time probably covered more ground than the German defender.
Andreas Christensen
See above. Will have been delighted to get an untroubled 90 minutes under his belt as he continues to struggle for regular minutes.
Like Rudiger, knocked the ball around well at the back but with very little purpose.
Emerson Palmieri
Desperately tried to create and even got behind the Malmo back line before pulling the ball back but to no avail.
He knew full well a good performance could see him dislodge Marcos Alonso for the Manchester City game and may well have done enough.
N'Golo Kante
It was his lung-busting drive from midfield – after winning the ball in midfield – that essentially killed the tie.
Not only did he drive forward with pace and purpose but he executed his pass to Willian perfectly. Did the same again ten minutes later before Barkley was flagged off.
Mateo Kovacic
We may well moan about Jorginho in the central pivot role in midfield. But when Kovacic dropped in there, he struggled. Gave the ball away, lacked fluidity and will not start in that role on Sunday.
And thanks to Barkley's goal and an apparent muscle problem late on, may well not start at all.
Ross Barkley
Booked for cynical foul to stop counter attack but tried his luck with a couple of shots that did not threaten Dahlin. Had a goal ruled out but then scored a lovely free-kick to seal the win.
Will be interesting to see if Maurizio Sarri opts for Barkley or Kovacic to complete the midfield trio at Wembley. On tonight's viewing, it HAS to be Barkley.
Callum Hudson-Odoi
Tracked back well but gave ball away on edge of own box and was almost punished early on. After that, constantly got on the ball, drove forward and looked to be the creative spark in Eden Hazard's absence.
PSG and Bayern will no doubt have been pleased with what they saw, especially when he found the net late on.
Olivier Giroud
Scored his sixth goal of this season's Europa League when he broke the deadlock on 55 minutes – and he won't get too many easier in his career than his right-footed finish from a yard out.
Will have given his boss a serious dilemma ahead of the final but is still likely to miss out to Gonzalo Higuain up front.
Willian
On his 200th Chelsea start, the Brazilian put the ball on a plate with his first-time cross for Giroud to open the scoring after Kante's fine piece of play.
That may well have secured his starting spot in Sunday's final, especially as he ended the game with the captain's armband.
Subs
Ruben Loftus-Cheek (for Kante, 76 mins)
Given a cameo run out but is sure to start on the bench on Sunday. Had a chance in injury time but hit the keeper.
Jorginho (for Barkley, 76 mins)
A gentle stretch of the legs for Sarri's linchpin for the final quarter of an hour. Protected to be at his passing best on Sunday.
Ethan Ampadu (for Azpilicueta, 79 mins)
Came on at right-back and was beaten immediately but recovered well and will have benefited from more first-team action. Could be a rogue substitute late on Sunday if holding on for an unlikely win.
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