After coming into the game 1-0 down on aggregate to Bayern Munich, Frida Maanum drew Arsenal level in the tie with a stunning first-time hit from 20 yards into the top corner after a clever back-heel from Leah Williamson.
And just seven minutes later, the Gunners were on top after Stina Blackstenius doubled the lead with a powerful header from six yards after a pinpoint cross from Katie McCabe.
Victory for the home side brought an end to Bayern's 14-game winning streak in all competitions.
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