Elsewhere, Real Madrid sealed a place in the knockout stages by beating Paris St Germain 1-0 in the Spanish capital.
Real have 10 points from four games followed by PSG on seven. Shakhtar and Malmo have three points and both the Ukrainians and the Swedes seem unlikely to progress.
Oleksandr Gladkyy netted in the first half before captain Darijo Srna (penalty), substitute Eduardo and Alex Teixeira killed off Malmo after the break in a one-sided encounter at the Lviv Arena.
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"Malmo should be pleased they only conceded four goals because we had so many scoring chances," Shakhtar coach Mircea Lucescu told reporters.
"We showed football is not only about the long balls Malmo are used to playing."
Gladkyy opened the scoring in the 29th minute when he knocked the rebound into the roof of the net after his first attempt was parried by keeper Johan Wiland.
Defender Kari Arnason then brought down Brazilian Teixeira three minutes after halftime and Srna converted the spot kick.
Eduardo, who replaced Gladkyy at the start of the second period, redirected a long-range shot from Bernard into the net to make it 3-0.
Teixeira completed the rout with a header in the 73rd minute after good work from Srna and Taison.
The only negatives for Shakhtar were the yellow cards received by defenders Srna and Oleksandr Kucher that mean they will be suspended for the next game against Real.
Malmo had Arnason sent off one minute from time.
"We did not look good from the very beginning of the game, we allowed them too much space," said visiting coach Age Hareide.
(Editing by Tony Jimenez)
