Mikel Arteta said the decision to award Sunderland a penalty could have cost Arsenal the Premier League title, even though his side emerged 2-0 winners at the Stadium of Light on Saturday.
Sunderland had the chance to take the lead early in the second period when Ezri Konsa was penalised for wrestling Dan Ballard to the floor.
Arteta was furious as pictures showed Ballard was also pulling the England international as the pair fell to the ground inside the Arsenal box.
The decision ultimately mattered little as Enzo Le Fee's spot-kick was brilliantly saved by David Raya.
Just two minutes later Bruno Guimaraes blasted Arsenal in front with his first goal for the club before Bukayo Saka's penalty sealed all three points in stoppage time.
But the result did not hold back Arteta's ire towards the officials.
"We have to go through what was done today that in my opinion is not acceptable. I watched it 20 times and I cannot find a way to understand how they think to give a penalty in that situation or the way the VAR has not intervened," said Arteta.
"I don't know what to think really. I'm sad that we have to discuss in such a beautiful game something at this level that has the gravity of that because that changes the course of the season and it can cost you the championship.
"At this level, with all the work that we put in, this cannot happen."
Guimaraes was Arsenal's big-money recruit of the transfer window, but the £75 million ($87 million) signing is yet to start for his new club as Arteta has kept faith with Myles Lewis-Skelly alongside Declan Rice and Martin Odegaard in midfield.
The Brazilian was introduced at halftime and proved his worth with a brilliant strike to break the deadlock and silence the Sunderland fans that took aim at the former Newcastle captain.
Guimaraes also had a hand in Arsenal's second goal as from his pass, Saka was chopped down for the penalty.
"The personality that he has. He comes in and this is a special game for him as well, what it means for him, and how he grabs the game," added Arteta.
"The decisions that he's made and the two actions. The goal is incredible and the assist as well to Bukayo to put him through in front of goal, it's unbelievable as well."
A fourth win from four Premier League games takes the defending champions three points clear at the top of the table.