The Canaries were penalised for encroachment after Tim Krul saved Pierre-Emerick Aubameyang's first-half penalty and the Gabon international made them pay by slotting home at the second time of asking.
VAR came to the Gunners' rescue by alerting the match official to Max Aarons overstepping the mark, but Farke did not think it was a just outcome.
"Yes the penalty (for Christoph Zimmermann's handball) was probably the right decision, but to replay it I think was strange," said the City boss.
"You will find something in the rules about why it should be replayed because Max Aarons' foot was in the box, but Arsenal's players were quicker than ours. Even if he started 10 inches later, he still would have cleared the ball so it didn't affect it at all.
"We were told at the start of the season if you are stood on the six-yard line at a penalty then that of course affects the game. Or three yards inside.
"But a part of my player's body was in the box along with Arsenal players."
Farke went on to protest that Arsenal striker Alex Lacazette's head was inside the penalty area for the re-take and that there were two balls on the pitch at the moment Aubameyang scored his side's second equaliser.
The ongoing feeling of injustice inside Carrow Road stems from the time Manchester United were awarded two VAR penalties against Norwich earlier this season.
Referees' head Mike Riley later publicly admitted the first of those was incorrectly given by VAR officials, although Norwich benefitted from the system not working correctly in September when West Ham should have had a penalty when Sebastien Haller was brought down by Tom Trybull.
"I was not happy with the quality of the decisions in this period of the game," he said. "It felt like each 50:50 call, each duel, each doubtful throw or corner or free kick went against us. The free kick that led to the penalty for me was never a free kick.
"When you speak to the fourth official it is like, 'yes, but it was just a throw in or a corner or a free kick,' but that can change the world in football."