The north Londoners lacked the presence of Gabriel Magalhaes as Carlo Ancelotti’s Toffees took advantage in the air to seal three points courtesy of a Rob Holding own goal and a Yerry Mina header either side of a Nicolas Pepe penalty.
With Gabriel and Granit Xhaka already unavailable due to suspension, Arteta was dealt a further blow with captain Pierre-Emerick Aubameyang missing the trip with a calf injury.
Everton looked the more confident of the two sides in the opening exchanges, and were rewarded as Dominic Calvert-Lewin headed Alex Iwobi’s cross off Holding and into the bottom right-hand corner of Bernd Leno’s net.
Still, Arsenal rallied and had a golden chance after Ainsley Maitland-Niles cleverly won a penalty after being caught by Tom Davies in an attempted clearance.
With Aubameyang out, Nicolas Pepe duly stepped up and calmly sent Jordan Pickford the wrong way to level the scores.
The Gunners were growing into the game, but were caught by a sucker-punch late in the half.
Leno made a superb save to deny Calvert-Lewin from range, but Everton took advantage from the resulting corner as Mina powered a header home at the near post with Arsenal’s defence static.
The loss puts more pressure on Arteta, and leaves Arsenal 15th in the table having played more games than the teams below them.