The Gunners left Madrid with the tie finely poised at 1-1 in the semi-final first-leg against Atletico Madrid.
Earlier in the match, Arsenal had taken the lead through a Viktor Gyokeres penalty in the 44th minute after the striker was fouled by the same player, David Hancko.
However, Atletico drew level in the 56th minute when Julian Alvarez converted a spot-kick of his own after being awarded for a handball against Ben White.
Arteta angry with VAR call
Arteta was left seething after a late penalty, initially awarded for a foul on Eberechi Eze, was overturned following a lengthy review.
With the score level, Eze was brought down inside the area by Atletico defender David Hancko. The referee pointed to the spot, but after consulting the pitch-side monitor, he reversed his decision, much to Arteta's disbelief.
"I am incredibly fuming with how the hell the penalty on Eze gets overturned in the manner that it happened when it’s so clear and obvious," a visibly angry Arteta stated post-match.
"It’s a clear contact; he made the decision, and you cannot overturn that decision when you have to look at it 13 times."
The Arsenal boss argued that the intervention fundamentally altered the outcome of the match and the tie itself.
"It changes the course of the game at this level. I’m sorry, but this cannot happen. It is completely unacceptable," he continued.
"When you have fought so hard for nine months to be in this position... That’s another goal that completely changes the course of the tie, and it cannot happen. We put so much into it. So, so much on it. This cannot happen."