Anthony Gordon's fourth goal of the campaign - in front of England manager Gareth Southgate - gave United the three points, while an eighth clean sheet in all competitions for the Magpies ensured the victory.
Before the game, both sets of players honoured service personnel past and present with a minute's silence, while the two teams wore poppies on their shirts.
In a feisty first half low on goalmouth action but high on incident Takehiro Tomiyasu and William Saliba saw shots deflected off target for the Gunners before, in the 29th minute, a cleverly-worked free kick was eventually floated by Bruno Guimarães towards the far post and headed back across goal by Dan Burn but Callum Wilson fired over, although the flag was up against Burn.
Tempers had flared on a handful of occasions throughout the opening 37 minutes but boiled over between players and the two dugouts when Kai Havertz flew in with a reckless challenge on Sean Longstaff, who was left writhing in agony.
Referee Stuart Attwell raced over to brandish a yellow card - then booked Longstaff, Gordon and Fabian Schär for protesting.
When play resumed, Gordon teed up Guimarães to shoot wide from outside the box, then shortly before half time, Gabriel Martinelli jinked into the opposite penalty area, evaded a desperate tackle from Kieran Trippier, but shot straight at Nick Pope.
Burn was forced off at the break with an apparent lower back injury - he was replaced by Tino Livramento - and the game continued in a similar vein, with few chances but a tense, spiky undercurrent, until the hour mark when Newcastle took the lead.
Joelinton bustled his way through and found substitute Jacob Murphy, who flashed across goal from a tight angle on the right. Fellow sub Joe Willock did superbly to keep the ball in play near the opposite corner flag and sent the ball back into the box, where Joelinton knocked it into the path of Gordon, who finished from close range.
With heavy rain now falling, a bizarre VAR check then unfolded with no less than three potential offences - ball out of play, a foul and an offside - checked and dismissed before the goal was finally given.
Murphy had to come off after seemingly aggravating the shoulder injury he suffered against Borussia Dortmund last month, with Matt Ritchie coming on for his 200th appearance for the Magpies.
Eddie Howe, already missing a number of key players, will hope that neither Murphy or Burn are sidelined for long - and he will be without Guimarães for next weekend's trip to Bournemouth after the Brazilian was shown a fifth booking of the campaign late on - but was able to celebrate a second hugely impressive win in four days.
