In Stockholm, first blood went to visitors Sirius midway through the first half, when Neo Ozzy Jonsson drilled the ball across the goalkeeper an into the bottom corner.
That's how things stayed until 10 minutes after half-time, when Noah Persson's low cross from the left wing was steered beyond the goalkeeper by Markus Karlsson to draw Hammarby level.
Just six minutes later, Bajen had completed the turnaround when Montader Madjed cut in from wide on the right and sent a beautiful curling effort out of David Celic's reach.
But chasing their maiden cup final, the Uppsala side would not be content with going down without a fight, and 12 minutes from time a corner was flicked on to the back post, where Robbie Ure was waiting to nod it home, sending the game to extra time.
Six minutes into the extra 30, Sirius took the lead for the second time when Isak Bjerkebo's sprint into the box caused pinball to ensue, before it finally fell kindly for Joakim Persson to pass into the empty net.
But once again, the visitors' lead didn't last, and in stoppage time at the end of the first half of extra time, a cross intended for Paulos Abrahams dropped into the path of Nahir Besara, whose turn and volley from six yards sent the match to a penalty shootout.
A tame first penalty for Sirius from Mohamed Soumah was saved by Warner Hahn, and after Hammarby scored their first four, Marcus Lindberg had to score, but again Hahn guessed right to win the shootout 4-2 and send 2021 winners HIF through to their sixth final in total.
There was less drama at Strandvallen, where league champions Mjallby kept the hunt for a double alive with a 3-0 victory over GAIS to reach the final for the second time, following defeat to Hacken in 2023.
With half an hour gone, Viktor Gustafsson found Tom Pettersson on the edge of the area, and the centre-back produced a first-time curling effort that a striker would be proud of to put MAIF ahead.
Late in the half, Jeppe Kjaer was brought down by a nasty Matteo de Brienne challenge inside the box, and Elliot Stroud did the honours from the penalty spot.
And Mjallby's place in the final was confirmed 10 minutes after the break, as GAIS failed to clear a free-kick launched into their box, allowing Jacob Bergstrom to execute a neat chest and volley from 10 yards out that nestled in the bottom corner.
The Mackerels failed to reach the final for the first time since 1987, instead, Mjallby will travel to 3Arena in the capital to face Hammarby on 14th May.