Pierre-Emerick Aubameyang doubled the lead just short of the hour mark, running onto a pass from former Borussia Dortmund team mate Henrikh Mkhitaryan and rounding the keeper to slot the ball home.
Petr Čech recorded his 200th Premier League clean sheet and saved his first penalty for Arsenal to boot.
The result leaves the Gunners sixth, 10 points behind fourth-placed Tottenham in the final Champions League spot.
Arsenal picked up a vital win in their pursuit of a top four finish with a dominant win over Watford.
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Although the Gunners second goalscorer of the evening Aaron Ramsey was not in the squad and Jack Wilshere benched. There were a lot of empty seats at the Emirates as fans showed discontent with the Arsenal hierarchy by staying away.
Rob Holding was a bit more forthcoming when he was asked about Deeney's comments, and agreed of course it affected the Arsenal players ahead of today's match.
Five minutes later Arsenal went 1-0 up on eight minutes. The Germany midfielder became the fastest man to reach that milestone - in 141 games - when Mustafi headed his precise free kick back across goal in the eighth minute.
Alex Iwobi fired a shot over the bar, while Roberto Pereyra wasted a golden opportunity, missing from a rebound after Cech couldn't clear the initial effort.
Not three minutes had passed when Mohamed Elneny and Mesut Ozil combined, the latter playing Pierre-Emerick Aubameyang through only for his low drive to enter through Karnezis's open legs but clip his underside and bounce up and wide.
As good as Arsenal was going forward, it was vulnerable at the other end.