The Premier League side went into the second leg holding a 2-1 advantage, and second-half goals from Olivier Giroud, Ross Barkley and Callum Hudson-Odoi sealed a comfortable win for under-pressure Maurizio Sarri.
Chelsea had been going through the motions but with six minutes remaining, Hudson-Odoi capped the ideal night for the Blues by drilling a low effort into the far corner of Dahlin's net from 12 yards out.
When asked what Hudson-Odoi needs to do to start in the Premier League, Sarri said: "You need to understand that, in the same position, we have Pedro, Willian and Hazard, so it's not easy for a young player to play with the consistency with his team-mates". Sarri has won 28 of his first 43 matches in England; the Spaniard had won 27 at the same stage.
Rudiger insists Chelsea can not look beyond Malmo - the Blues hold a 2-1 first-leg advantage in their last-32 tie - but admits Sarri's Chelsea face a day of reckoning at Wembley on Sunday. Jorginho came on for Barkley to boos.
Speaking after the match, Hudson-Odoi said: "I'm happy with the result".
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If the use of Kante was a feather in Sarri's cap, his sparing deployment of Hudson-Odoi was once again shown up, at least in the home supporters' eyes.
Sarri might like to point to the first-half error which led to a Markus Rosenberg shot whistling past the post, which would have given Malmo the lead.
Consequently, the former Napoli Coach would be the Giallorossi's "first choice" to take the reins, given his own insecurities at Stamford Bridge.
Jorginho has struggled badly at times when targeted by other teams, leading many to call for Kante to be restored to his favoured role, but Sarri has revealed that he does not think the France worldwide can pass the ball fast enough to suit his system.
'The 20 matches in this season will become 30 in the next, then 40 in two years.
Jorginho has been below par since signing and Sarri says the player is better than they think he is.