Arsenal, the 2019 finalists under Unai Emery, were struggling to make an impact in Austria.
After a goalless first half they went behind when keeper Bernd Leno fluffed a clearance on a night he will want to forget.
Taxiarchis Fountas capitalised on Leno's clanger, much to the joy of the 3,000 home fans allowed in to watch under coronavirus safety protocol, but the Gunners then turned the game around in four second half minutes.
David Luiz put them level with a deft glancing header off Nicolas Pepe's free-kick, with Pierre-Emerick Aubameyang then tapping home to bag the three Group B points.
It was an eventful night for Mikel Arteta's side with alongside eight yellow cards an eye catching display from Thomas Partey on his first start since his transfer deadline day move from Atletico Madrid.
A frustrated follower of the game from his London sofa was Mesut Ozil, who has been left out of both Arsenal's Europa League and Premier League squad.
"When I can't support on the pitch tonight, I will support in front of the TV in London." tweeted Ozil.
The other Group B game was being played out in Dublin where Dundalk, only Ireland's third ever representative in the group stage, were beaten 2-1 by Norwegians Molde.
In Belgium, Steven Gerrard's Rangers took on Standard Liege fresh from their Old Firm derby win over Celtic which moved them four points clear in the Scottish Premiership last weekend.
With the rain coming down, James Tavernier scored from the spot after Noe Dussenne handled in the area to put them into a 19th minute lead.
Then three minutes into stoppage time Kemar Roofe produced a wonder goal from the halfway line, the ball flying over the head of bewildered keeper Arnaud Bodart.
Benfica had claimed the first goal of the night and they went on to beat Lech Poznan in Poland 4-2 in the other Group D game.
Elsewhere, Bayer Leverkusen ran riot 6-2 against French side Nice and Spanish side Granada, in their first ever European campaign, beat PSV Eindhoven 2-1.
Later, Tottenham host Austrian side LASK with Gareth Bale making his first start since returning to Spurs on a season-long loan.
Seven-time European Cup winners AC Milan are at Celtic, and Leicester host Zorya Luhansk of Ukraine.
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