In a meeting between two teams hoping to challenge for the 2025 Allvenskan title, nothing could separate the teams over 90 minutes.
It was the home side who were ruing missed opportunities, though, as they dominated the shot count but could not find a way past Elfsborg goalkeeper, Isak Pettersson, who made six saves in normal time.
Yet, it only took six minutes of extra-time for the pressure to finally tell, when Taha Ali was fouled inside the penalty area.
Isaac Kiese Thelin stepped up and converted the penalty to give The Blue Ones the lead with his second goal of the competition.
No shots on target in response from the visitors meant the spot-kick was enough for Malmo to reach a third cup Semi-final in four years - on the previous two occasions, they went on to lift the trophy.
But if the Quarter-finals are anything to go by, then they face a serious challenge in the last four next week, at home to Goteborg, who thrashed Hammarby 4-0 on Sunday.
Midway through the first half, Tobias Heintz's corner somehow evaded everyone in the crowded penalty and sneaked in past goalkeeper Warner Hahn to put the home side ahead.
After 32 minutes, the lead was doubled thanks to a quick counter-attack, finished off by Eman Markovic.
Inside the final 20 minutes, Markovic scored his second of the game, steering the ball into the bottom corner as Hammarby failed to deal with constant pressure inside their box.
Late on, the Norwegian completed his hat-trick with a curling right-footed strike, having been picked out with a lovely ball forward from Sebastian Clemmensen.
Only Malmo with 16 have more Svenska Cupen titles than Goteborg's eight.
Trying to stop either of them from adding to their titles will be six-time winners Norrkoping and three-time winners Hacken, who meet in the other Semi-final.
Norrkoping were up against Trelleborg, the only second-tier side who made it to the knockout stages.
The visitors' fairytale run looked to be continuing on Sunday when Felix Horberg gave them the lead late in the first half, only for Tim Prica to equalise two minutes after the break.
Trelleborg took the tie to extra-time, but their chances of another shock took a turn for the worse when Tobias Karlsson was dismissed in the 89th minute.
The extra 30 minutes a man down was too much for the Superettan side, who conceded to Sebastian Jorgensen and Isak Sigurgeirsson to hand Norrkoping a 3-1 win.
On Saturday, late drama handed Hacken their place in the last four, as Samuel Leach's 94th-minute free-kick was bundled in at the back post by Abdoulaye Faye to beat Mjallby 1-0 away from home.