In the first leg of their qualifying second-round battle, the Gunners succumbed to a second-half Tabby Tindell winner against their Scandinavian hosts, whose pressure paid off after Arsenal failed to make the most of theirs.
Jonas Eidevall's team had ruthlessly dispatched Rangers 6-0 and edged out Rosenborg 1-0 to earn a second-round date with Hacken, whom they beat 3-2 on aggregate back in the 2011-12 quarter-finals.
However, Arsenal struggled to properly adapt to the artificial turf at the Bravida Arena, although they still gave their Swedish foes plenty to think about, just without the desired end product.
Beth Mead was left to rue one gilt-edged chance in the second half, smashing the ball into the face of Hacken goalkeeper Jennifer Falk with a header from point-blank range, and the clincher arrived 13 minutes from the end of normal time.
After Katie McCabe failed to deal with a hopeful punt forward, Tindell capitalised on her swipe at thin air to charge through on goal before a delicate dink over the onrushing Manuela Zinsberger.
Eidevall's side must now turn the team on its head at Borehamwood in next Thursday's second leg, prior to which they kick off their new Women's Super League season at home to Manchester City on Sunday lunchtime.
The Citizens were also in Champions League qualifying action tonight and fared far better than their capital counterparts, smashing Paris FC 5-0 with a goal from ex-Arsenal attacker Vivianne Miedema.