Stanislav Dragun's brilliant header on 45 minutes earned BATE only their second ever victory over Premier League opposition – ten years after a 1-0 triumph at Everton.
Yet the Gunners – who will still be strong favourites to go through on aggregate – dominated before the interval.
Henrikh Mkhitaryan somehow slid a Sead Kolasinac cross wide from the middle of the six-yard box in just the second minute.
And Shkodran Mustafi soon headed Mkhitaryan's centre wide – while Lacazette nodded high midway through a one-sided half.
Kolasinac missed another inviting chance on 42 minutes – but BATE stole ahead almost on the whistle from just their second clear chance of the 45 minutes.
Igor Stasevich ambled up casually to swing in a routine free-kick from the right that Dragun flashed home from the near post to the far bottom corner.
And as the pitch cut up in the second period the tie turned into something more like a blood-and-thunder FA Cup game – frustrating Arsenal still further.
But it got much worse as Lacazette – who also had a goal disallowed – got a straight red for swinging an elbow into the face of a defender who was holding him back on the half-way line.
That means Lacazette will be suspended for the return leg, when surely the Gunners will step up at least two gears.
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