Ozil had missed the Carabao Cup defeat by Spurs for “tactical reasons” but played a big part in setting up Aubameyang for the opening goal.
When the Arsenal striker made it 2-0 early in the second half, the contest looked over apart from the tasty challenges which led to a number of yellow cards.
But Burnley kept battling, pulled one back through Ashley Barnes and could have snatched a point as the Gunners once more failed to keep a clean sheet.
Only a stoppage-time goal by Alex Iwobi, set up by Ozil, settled Arsenal's nerves.
The game started at breakneck pace.
In the second minute, Joe Hart made a good save from Ainsley Maitland-Niles. From James Tarkowski’s brave follow-up clearance, Burnley went straight down the other end, where Ashley Westwood’s shot was deflected behind by Arsenal goalkeeper Bernd Leno.
But chances for Granit Xhaka and Mohamed Elneny suggested an Arsenal goal was coming and it soon arrived.
Ozil’s lovely pass found Sead Kolasinac arriving at the back post and his touch back fell for Aubameyang, whose slightly mishit volley found the corner of the net.
A running battle between Barnes and Sokratis, which included a bit of wrestling, led to both being booked in quick succession but otherwise the game already seemed to be drifting.
The only worry for Arsenal was the loss of luckless Nacho Monreal, who went off injured having only recently returned to action.
Within three minutes of the restart, things looked even more straightforward for the hosts when Aubameyang lashed the ball into the net after a quick break involving Kolasinac and Alexandre Lacazette.
But Burnley were not finished. Sokratis had to make a vital challenge on Chris Wood and from the resulting corner, the visiting bench was screaming for a penalty for a push on Kevin Long by Kolasinac.
The away fans were shouting for a different reason a few minutes when Barnes lashed the ball into the net after a scramble in the box.
Cork missed a good chance to equalise with 20 minutes left and the needle which had always been in the game continued as Xhaka rowed with the Burnley bench after a foul by Westwood.
Left back Charlie Taylor slid a shot into the side netting but the Clarets were unable to find a second goal.
Instead, Arsenal broke in the first of five minutes of stoppage-time, Ozil twisted and turned in the box, and the ball broke for substitute Iwobi to fire into the net.
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