Arteta's side left San Siro empty handed, with Hakan Calhanoglu's penalty separating the sides, and condemning Arsenal to a second away defeat this week.
The penalty itself seemed dubious to some, given for a handball by Mikel Merino, who according to Arteta, should have been awarded one himself at the other end following an erratic punch from Inter's Yann Sommer.
There was concern before the game for the Gunners too, as Declan Rice missed out entirely for precautionary reasons and will be assessed ahead of the trip to Chelsea on Sunday.
Havertz a doubt for trip to Chelsea?
As the clock ticked towards 90 minutes, an in-swinging cross looked inviting for Havertz, but fine defending from Yann Bisseck saw the German compatriot get to the ball first, and head to safety.
Unfortunately for the Arsenal attacker, he clashed heads heavily with the Inter defender, and immediately hit the floor in some discomfort, with Inter keeper Sommer quickly pleading for help from the sidelines.
The German was down on the turf for almost three minutes, receiving attention from the Arsenal medical staff, before being replaced by the returning Martin Odegaard.
As Havertz trudged off around the side of pitch, the extent of the injury was clear, as blood continued to pour from his head, had run all down his face, and even onto the training jacket of the Arsenal physio treating him.
Thankfully, Havertz was pictured leaving the press area without any bandaging around his head, but concussion protocols will be considered before a decision is made about including him in the squad at the weekend.
Arsenal injury situation ahead of trip across London
The defeat in Milan tonight means that Arsenal will be under intense pressure to pick up a positive result at Stamford Bridge on Sunday.
Having also lost against Newcastle United in the Premier League last weekend, the Gunners could find themselves 10 points adrift of Liverpool heading into the international break if they lose for a third straight game.
With Rice doubtful, and Havertz now questionable with a head injury, Arteta has issues in all areas of the pitch, with Riccardo Calafiori and Takehiro Tomiyasu also missing at the back.
The only positive from their evening in Northern Italy was the return of captain Odegaard slightly ahead of schedule, who got a few minutes under his belt.
It is unlikely Odegaard will be thrown in straight away against Chelsea either, but if the club can keep him at London Colney over the international break, he should be fit and firing ahead of a busy festive period.