Both London clubs will play away from home in the first leg which is to be played on February 14 as the duo were handed favourable ties.
The Gunners faced Belarusian side BATE in the group stages of the Europa League last season, where they easily won both games.
A 4-2 away win was followed up with a 6-0 demolition at the Emirates, with Arsenal to go into the game as heavy favourites.
Gooners were delighted with the draw, with fans predicting an easy win against Alyaksey Baha's men, where they will come up against former fan favourite Alexander Hleb.
BATE were in Chelsea's group this season, where they lost both times against the Blues.
Maurizio Sarri's side will come up against Malmo in what will be the first competitive match between the two.
And Chelsea fans have claimed it will be a "walk in the park" for their club as they predict a routine victory.
Malmo – who finished second in Group I – secured their place in the knockout stage by beating Besiktas 1-0 in Turkey last week.
Scottish giants Celtic have been handed a nightmare draw against La Liga outfit Valencia.
EUROPA LEAGUE DRAW
- Viktoria Plzen vs Dinamo Zagreb
- Club Brugge vs Salzburg
- Rapid Wien vs Inter
- Slavia Prague vs Genk
- Krasnodar vs Bayer Leverkusen
- FC Zurich vs Napoli
- Malmo vs Chelsea
- Shakhtar Donetsk vs Eintracht Frankfurt
- Celtic vs Valencia
- Rennes vs Real Betis
- Olympiakos vs Dynamo Kiev
- Lazio vs Sevilla
- Fenerbahce vs Zenit
- Sporting Lisbon vs Villarreal
- BATE Borisov vs Arsenal
- Galatasaray vs Benfica
Brendan Rodgers' side only qualified after RB Leipzig were held to a draw against Rosenborg, and know they must be on the top of their game against the Spaniards.
Serie A side Lazio were pitted against Sevilla in one of the standout ties of the Round of 32.
While Sporting Lisbon were matched against Villarreal and Galatasaray were drawn against former runners-up Benfica.
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