The Gunners had the chance to temporarily move 10 points clear of Manchester City at the top of the table last week, but they were held to a 0-0 draw by the Magpies.
During the fifth minute of second-half injury time, Granit Xhaka's attempted cross was blocked by the arm of Jacob Murphy at close range, leading Arsenal players to scream for a penalty.
Mikel Arteta's men surrounded referee Andy Madley during their zealous appeals, while the Arsenal boss cut a furious figure on the touchline, but neither Madley nor VAR official Stuart Attwell was swayed.
Arteta hit out the "scandalous" decision after the game, having also seen a tug on Gabriel Magalhaes by Dan Burn waved away, saying: "It's not about stronger, it's two penalties. That's very simple. I'm talking about what I've seen now. It's two scandalous penalties.
"We had a lot of situations around the box to do better and then those penalties. Both of them. It's not particular. It's a penalty or not a penalty and these are both penalties.
"I feel the team was on top, we were chasing it, we really wanted it. You could see the team was doing everything to win it. We lacked that in the final third and then we lacked the two big decisions obviously."
Following Arsenal's appeals for the last-minute penalty, the club was charged with failing to ensure their players conducted themselves appropriately, and they have been hit with a hefty fine after admitting the offence.
A statement read: "Arsenal FC has been fined £40,000 for breaching FA Rule E20.1 during its Premier League fixture against Newcastle United FC on Tuesday January 3 2023.
"Arsenal FC admitted that it failed to ensure its players conducted themselves in an orderly fashion during the 95th minute. An independent Regulatory Commission imposed the club's sanction during a subsequent hearing."
The Premier League leaders were hit with a second conduct charge in the space of a week on Thursday after also appealing for a handball in their FA Cup third-round win over Oxford United on Monday.
In the first half of that 3-0 win, Albert Sambi Lokonga's shot was blocked by the hand of Elliott Moore, leading the Belgian and a few other Arsenal players to surround David Coote and ask for a penalty.
A spot kick was ultimately not awarded, and Arsenal have until Monday to respond to that charge, which was brought up to Arteta during Friday's pre-North London derby press conference.
However, the 40-year-old refused to comment on the ongoing case, saying: "I prefer not to comment. Anything we can do to improve, we always have conversations with our players and with our staff to see what we can do better and if we have to improve our behaviour."
Arsenal enter Sunday's derby with Tottenham Hotspur winless at Spurs' new ground in three games, as they aim to maintain or increase their five-point lead over Man City at the summit.