Alexandre Lacazette featured amongst a host of changes and also captained the Gunners who gave Thomas Partey his first start and issued rare appearances for Cedric Soares and Sead Kolasinac.
Arsenal were metres away from the deadlock in the opening 15 minutes when a galloping header from the back-post by David Luiz had Richard Strebinger scrambling to parry.
Gabriel Magalhaes made a timeous block to divert a back-heel attempt from Marcel Ritzmaier five minutes later crippling past Arsenal goalkeeper Bernd Leno.
Rapid finished the first half the strongest after Dejan Ljubicic flashed across the far corner following a ball at the near post and put Leno under further pressure from a ball by Ritzmaier.
A goalkeeping error from Leno gave Rapid the lead on 51 minutes with a move from the back quickly seized by Taxiarchis Fountas to slot into an empty net.
Another error from Leno later on allowed Fountas in again, but luckily the German international recovered quickly to smother the forward.
The Gunners tried a turnaround from the substitute's bench 61 minutes in as Hector Bellerin and Pierre-Emerick Aubameyang came on for Cedric and Eddie Nketiah. It proved to be a masterstroke inside nine minutes after Luiz leaped onto a curling free-kick from Nicolas Pepe to head into the bottom-corner.
The substitutes combined to complete the turnaround in less than three minutes when a square ball from Bellerin landed to an unmarked Aubameyang to tap into empty net.
Arsenal still pushed for a third goal in the remaining stages of the match, but 2-1 was how the encounter finished.
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