Samuel Adegbenro needed just two minutes to break the deadlock.
The striker bumped into an Arí Skulason's perfect post - and driver's seat for IFK Norrköping directly.
The visitors kept the pressure on to tie the game when, after 24 minutes, Adegbenro broke through the center and found himself alone with the keeper.
He got the forehead on a post from Carl Björk, but Bajen's young goalkeeper Oliver Dovin tipped the ball over.
Two minutes later it turned the other way.
Astrid Selmani stepped into the penalty area and recorded the ball to Gustav Ludwigson who ice-coldly heeled the ball behind Oscar Jansson.
Saved by Paulsen
With 66 minutes played, Selmani's Vladimir Rodic almost extended the lead, but his shot from the left glanced off the top of the bar to fall behind the net.
Four minutes later it was again about Adegbenro.
The hungry player accelerated towards Hammarby's back line and walled with Maic Sema to get into the penalty area - but ended up at a worse angle and got away with a finish that Dovin saved.
Then it was Hammarby who would find a decisive goal.
With 83 minutes played, Björn Paulsen of FC fell dramatically just outside the penalty area. However, the referee was unimpressed, and booked him for diving.
A goal that won the match.
Hammarby takes its third straight victory and meets Östersund in the next round.
For Beijing, IFK Gothenburg is waiting away.