The Stockholm side began the day two points behind Group 4 leaders Goteborg, knowing only the group winners would be advancing to the Quarter-finals.
But they found themselves behind in the 12th minute, when Imam Jagne was left unmarked on the edge of the six-yard box and he made no mistake with his header.
The Blue Stripes responded well and were in front after 40 minutes, thanks to a well-taken strike under pressure by Nino Zugelj to equalise, and Oskar Fallenius steering the ball home after IFK had coughed-up possession deep inside their own half.
However, they were unable to take the lead into the break, as the visitors made it 2-2 in the final minute of the first half.
Goalkeeper Jacob Rinne could not gather Eman Markovic's effort and spilled the ball at the feet of Max Fenger, who tucked home from close range.
Midway through the second half, the lead swung back The Angels' way, when Fenger was again in the right place for his second tap-in of the match.
Thomas Santos sealed the win four minutes from time to send Goteborg through with maximum points from their three group matches and reach the last eight for the first time since 2022.
Coincidentally, that was the last time before today that Djurgarden failed to reach the quarter-finals.
No one got a touch on Keita Kosugi's cross which drifted all the way in in the 96th minute to complete the scoring.
The other game in Group 4 saw Sandviken move off the bottom with a 1-0 win over Oddevold, who finish the group with one point.
Holders Malmo safely through
Allsvenskan and Svenska Cupen holders Malmo are safely through to the quarter-finals with maximum points with a 3-0 victory over Vasteras SK in Group 1.
Former Brentford man Pontus Jansson gave The Blue Ones the lead early in the second half and when Erik Botheim scored six minutes later, there was little hope of the Superettan side pulling off a shock.
Lasse Berg Johnsen made sure of the win in the 73rd minute for the champions.
A 2-1 win for Utsikten over Skovde AIK meant they finished third, three points behind Vasteras.
Mjallby are also part of the lineup for the last eight, topping Group 5 in style as they also won a winner-takes-all clash 3-0, making no mistake at home to Halmstad.
The team from Hallevik also had to be patient, but cometh the hour, cometh the Manneh - Abdoulie Manneh put the hosts ahead just shy of the hour mark.
Jakob Kiilerich added the second before Tom Pettersson put the icing on the cake late on for the side who scored 12 without reply in their three group games.
10-man Landskrona won the battle for the minor places, beating Gefle, 3-1.
Incredibly, Group 6 also had a one-sided tie showdown for top spot, and it was Norrkoping who took it by beating GAIS 3-0 away in Gothenburg.
Tim Prica broke the deadlock before half-time, then two goals in five minutes late in the second half from David Moberg Karlsson and Christoffer Nyman rounded off a perfect afternoon for the visitors.
Karlbergs' 2-1 win at Orebro meant they finished third in the group.
Completing the final round of group stage fixtures, second-tier Trelleborgs' fairytale run continued as they won 1-0 away at Degerfors on Friday to win Group 3, two points clear of AIK.
Then, on Saturday, Elfsborg held off their Allsvenskan rivals Brommapojkarna with a 1-1 draw at home to win Group 7.
Group 8 turned out to be the tightest of them all, with Hacken prevailing on goal difference ahead of both Oster and Sirius, with all three sides finishing on six points.
Sirius beat Hacken 2-0 on the final matchday, but wins by three goals in their first two games were enough to see them through with a goal difference of +4.
Sirius finished with a goal difference of zero, while Oster finished second with +1 as they could only manage a 1-0 win over Helsingborg.
The Group Stage will be completed tomorrow with Group 2's final matches. Leaders Hammarby are only one point behind Kalmar, who they will host.
Stockholm Internazionale are in third on goal difference and they take on already-eliminated Varberg.
