Malmo came into the tie guaranteed of League Phase football, but after a 5-0 aggregate loss to FC Copenhagen in the UEFA Champions League last week, were keen on securing a UEL place and not drop down again into the UEFA Conference League.
However, they were under pressure right from the off against Sigma Olomouc, and needed goalkeeper Robin Olsen to produce two reaction saves at close range, first from Filip Slavicek and then Abdoulaye Sylla following up on the rebound.
But in the eighth minute, the home side took the lead, when a poor pass out from goalkeeper Jan Koutny was picked up by Adrian Skogmar, who diverted the ball towards Taha Ali. He slipped a perfectly-weighted pass through to Sead Haksabanovic and he finished in style.
Malmo had more of the ball and territory in the first half, but despite looking to get balls into the box, they didn't manage another shot until the 43rd minute. Yet that was all it took for MFF to double their lead.
Otto Rosengren's corner caused havoc in the Olomouc box, and Haksabanovic was on hand to rifle the ball into the roof of the net for his second of the night.
In the second half, the officials took centre stage, as first a VAR review determined Abdoulaye Sylla would not be sent off for a poor challenge, before Daniel Vasulin's strike on 62 minutes deflected off teammate Jan Navratil and past Olsen.
However, this time VAR came down on Malmo's side, disallowing the goal as Navratil was in an offside position.
Then, in added time, referee Tobias Stieler didn't need any help from his video assistants as he awarded a penalty for a foul on Emmanuel Ekong, committed by Sylla, who was fortunate to still be on the pitch.
With Haksabanovic substituted, it fell to Lasse Johnsen to take the penalty, which he planted into the top corner to give Malmo a 3-0 lead to take to the Czech Republic next week.