Arsenal welcomed Hacken to Borehamwood trailing 1-0 after suffering defeat on the road to the Swedes last Wednesday.
But strikes by Lia Waelti and new signing Mariona Caldentey inside 40 minutes gave Jonas Eidevall's side the lead prior to the break.
Beth Mead and Frida Maanum then put the tie beyond Hacken's reach as Arsenal ran out 4-0 winners.
Manchester City went into their home leg with a comfortable 5-0 advantage after a dominant first-leg display in Paris last week.
A goal after two minutes by England striker Chloe Kelly effectively put an end to any hopes of an unlikely Paris FC comeback, before Khadija Shaw scored just after the half-hour and hour marks to seal a 3-0 win.
Real Madrid won 3-1 at home to Sporting Lisbon, with a brace either side of half-time by Sandie Toletti and a goal in second-half stoppage time from Alba Redondo easing the Spaniards to a three-goal winning margin over both legs.
Last season's semi-finalists Paris Saint-Germain failed to overturn their first-leg deficit against Juventus as they lost 2-1 at home to the Italians on the night, and 5-2 on aggregate.
Roma emerged 10-3 aggregate winners as they overpowered Swiss side Servette Chenois 7-2 in the return fixture in Geneva.
Dutch club Twente romped into the group stage as they scored four goals in both ties against Croatia's Osijek on their way to an aggregate win of 8-1.
St Polten of Austria won 5-0 in Slovenia against Mura to complete an impressive 8-0 aggregate win.
Celtic won 2-0 against visitors Vorskla of Ukraine to go through 3-0 on aggregate.
On Wednesday, two-time champions Wolfsburg, Norwegians Valerenga, Sweden's Hammarby and Galatasaray sealed their places in the tournament proper.
Lyon, Bayern Munich, Chelsea and holders Barcelona all automatically qualified for the group stage of the Women's Champions League.
Now that all 16 group-stage spots have been decided, the draw will take place in Nyon, Switzerland on Friday.
