The Gunners' 11-game Premier League unbeaten run came to a painful end at St James' Park, where Anthony Gordon condemned the North London club to their first league defeat of the season.
However, Arsenal were on the wrong end of a handful of contentious decisions in the North East, as Bruno Guimaraes avoided a red card despite appearing to clearly elbow Jorginho in the head.
The Gunners had arguably got away with one themselves beforehand, as Kai Havertz's shocking challenge on Sean Longstaff was only deemed yellow-card worthy, before Gordon fired home from close range to settle the contest.
Newcastle's attack would seemingly break down as Jacob Murphy's shot headed for the corner flag, but ex-Arsenal man Joe Willock just managed to keep the ball in play before crossing into the six-yard box.
David Raya tried to palm Willock's delivery away and missed, allowing Joelinton to tower over Gabriel Magalhaes and nod down for Gordon, who could not miss from a yard out.
The VAR room was satisfied that Willock managed to stop the ball from going out of play, before also checking to see whether Joelinton had committed a foul on Gabriel, having seemingly had two hands on his fellow Brazilian's back.
Joelinton was not penalised, though, and Gordon was deemed to have been onside when his teammate's knock down reached him, as Newcastle's goal was eventually confirmed following no fewer than three separate checks.
There was no way through for a lacklustre Arsenal in the time that remained, and while the Gunners' performance left a lot to be desired, Arteta let rip during his post-game press conference, claiming that Newcastle's goal was a "disgrace".
The Spaniard also stated that he felt "sick" and "embarrassed" by the level of officiating in the Premier League, risking retrospective action from the FA in the process, but Arsenal have jumped to the defence of their head coach.
"Arsenal Football Club wholeheartedly supports Mikel Arteta's post-match comments after yet more unacceptable refereeing and VAR errors on Saturday evening," a statement read.
"The Premier League is the best league in the world with the best players, coaches and supporters, all of whom deserve better. PGMOL urgently needs to address the standard of officiating and focus on action which moves us all on from retrospective analysis, attempted explanations and apologies.
"We support the ongoing efforts of Chief Refereeing Officer, Howard Webb and would welcome working together to achieve the world-class officiating standards our league demands.
"We'd also like to acknowledge the huge effort and performance from our players and travelling supporters at St James' Park."
Arsenal's first league defeat of the season leaves the Gunners in third place in the table, although they could drop to fourth if Liverpool overcome Luton Town on Sunday, and a Champions League clash with Sevilla on Wednesday is next up for the North London giants.
VAR was also in the headlines during Wolverhampton Wanderers' loss to Sheffield United, where Gary O'Neil also lashed out at the standard of refereeing and VAR after Oliver Norwood's last-minute penalty won the day for the Blades.