The victory means neither of the sides to win the previous four editions have made it to the Semi-finals, after holders Hacken were eliminated in the Group Stage.
Record 16-time winners Malmo were reduced to 10 men, but only in 91st minute once the game had long been decided. The home side were 2-0 up inside half an hour through Elliot Stroud and then Jacob Bergstrom.
Another pair of strikes, within four minutes of each other either side of the hour mark from Bergstrom and Villiam Granath, settled the tie to send the 2023 finalists marching on and the record winners out, as Theodor Lundbergh's afternoon ended slightly early following a second booking.
Sirius are one game away from their maiden final, as one goal from the penalty spot was enough to send them through at the expense of Goteborg.
A goalless 90 minutes meant they needed extra time to settle it, and after Rockson Yeboah chopped down Isak Bjerkebo inside the area, Bjerkebo stepped up to score the winner from 12 yards.
The Uppsala side's opponents for a place in the final will be Hammarby, after they won a Stockholm derby 1-0 against Djurgarden to maintain hopes of winning the cup for the second time.
The designated visitors had no answer to a flowing Bajen move in the 91st minute, which resulted in Paulos Abraham coolly slotting home the winning goal.
Mjallby, meanwhile, will face GAIS in the last four, after the Mackerels came from behind to beat AIK 3-2 at home. Kevin Holmen's opener in the fourth minute was the only goal until after the hour mark, when the visitors swiftly turned things around through Zadok Yohanna and Johan Hove.
But GAIS hit back, with Holmen playing his part again, as he found Rasmus Niklasson to equalise with 13 minutes to play. In added time, Holmen notched another goal involvement when he found Shalom Ekong, who kept GAIS dreaming of a first Svenska Cupen win since 1942.
The semi-finals will be played on Sunday 22nd March:
13:30 CET: Hammarby vs Sirius
16:00 CET: Mjallby vs GAIS