Coming off an inspiring feat in midweek, where the striker's hat-trick helped his side into the final of the Europa League, Aubameyang scored two second-half goals at Turf Moor.
Burnley is an awfully long way from Baku - and not merely in miles - but Arsenal's final stop on the road towards Azerbaijan's capital and the Europa League final was not quite the meaningless detour it might have appeared.
It was two just past the hour, when Aubameyang volleyed home Mohamed Elneny's cross brilliantly, but Burnley hit back nearly straight away when Barnes headed home from close range.More news: Jimmy Butler proves once again why Sixers must give him the max
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The Gunners know they are set to finish outside the top four, but what they do at Turf Moor still matters as Manchester City are just a point and a place behind, in sixth, and Europa League qualifiers start in July.
Shkodran Mustafi's superb block thwarted Matt Lowton before Joe Willock fired narrowly wide late in the half but Arsenal were ahead seven minutes after the interval as Cork's ball evaded Ben Mee and allowed Aubameyang to beat Heaton.
In between Bernd Leno escaped unpunished after ending up tussling with Barnes after dashing out of his area.
Nacho Monreal and Pierre-Emerick Aubameyang are the only ones to keep their place. The goalkeeper went through the back of the Burnley man, but Dean didn't see it and booked him for his reaction. Arsenal lead through Aubameyang. Burnley hit straight back through Barnes, who heads in from close range after sustained pressure. Substitutes: Koscielny 5, Nketiah 6.