Richarlison drove to the byline and tried to slip it under the German custodian, but he fumbled the catch in a bizarre own goal.
It was the culmination of another poor performance from the Gunners, who struggled to break down a well-drilled Toffees side and came undone following another individual gaffe.
The loss keeps them in ninth position in the standings, six points off Everton, who even have a game in hand as the London side head towards their lowest points tally of the Premier League era.
Here are the player ratings for Arsenal
Bernd Leno - 5/10
It was turning out to be a routine night for Leno, who even made two fantastic saves on the night, but blew it all up in smoke with a huge blunder midway through the second-half.
Callum Chambers - 6/10
He was dangerous going forward, making a few good crosses, but came a cropper in the defense, giving Digne too much space to work into.
Rob Holding - 6/10
A mixed bag for the man who donned the captain's arm band. He dealt well with Calvert-Lewin and pulled a block on Sigurdsson. However, the full-back gave away some cheap fouls and made poor decisions in some key moments.
Pablo Mari - 6.5/10
Another resolute performance from Mari, who too played a key role in keeping Calvert-Lewin quiet and looked brilliant with the ball at his feet.
Granit Xhaka - 6/10
The Swiss was given a rough time by Richarlison and couldn't really go forward much because of the Brazilian's threat.
Thomas Partey - 6.5/10
He was the key to ball recovery for Arsenal and used his physical strength to win the midfield battle. However, the Ghanian was sloppy in possession and took a tad too long on the ball at times.
Dani Ceballos - 6/10
Ceballos drove forward with purpose and tried to poke holes in the Everton defense, but nothing significant came of it. The penalty he won was overruled and was also guilty of executing a godawful corner kick.
Bukayo Saka - 5/10
Arsenal were toothless in the attack, with Saka's minimal impact playing a part too. He struggled to get past Digne and just fizzled out after a bright start.
Emil Smith Rowe - 5/10
The Arsenal graduate was the worst of the lot, with Everton firmly keeping him under wraps.
Nicolas Pepe - 6/10
Pepe was crucial in building up play and worked well in tandem with Saka.
Eddie Nketiah - 5/10
The striker looked to be getting in behind Everton's defense with little success and didn't find much luck on the break either. He faded completely after the break.
Martin Odegaard - 5/10
Arteta brought him on to inject some attacking flair into the final 15 minutes of the game but the Norwegian was anonymous.
Willian - N/A
The Brazilian came on too late to make any impact for Arsenal.
Gabriel Martinelli - 6/10
He could've salvaged a point for Arsenal in the dying seconds had it not been for Pickford's instinctive save.