For much of the evening, Leverkusen were the sharper side.
The Bundesliga outfit had already shown glimpses of danger in the first half, particularly through 19-year-old striker Christian Kofane, who constantly harried Arsenal’s defence and even forced Gabriel into an early mistake.
Arsenal had a moment of promise midway through the opening half when Gabriel Martinelli crashed a powerful effort against the crossbar after a slick attacking move involving Eberechi Eze and Viktor Gyokeres.
But beyond that chance, the visitors struggled to convert possession into real danger.
The problems only intensified after the break.
Within moments of the restart, Martin Terrier forced a brilliant fingertip save from David Raya following a cross from Alejandro Grimaldo.
But the warning went unheeded.
From the resulting corner, Grimaldo delivered a looping ball to the far post where Robert Andrich was left completely unmarked. The German midfielder powered a header past Raya to give Leverkusen a deserved lead.