Newcastle end Arsenal's unbeaten run in controversial fashion
Mikel Arteta's side were defeated for the first time in 11 league games, with the Arsenal manager labelling the defeat "a disgrace".
Joelinton clearly pushed Arsenal defender Gabriel as the pair challenged for Joe Willock's cross, with the ball running for Gordon to score from close-range.
As well as appealing in vain for a foul by Joelinton, Arsenal angrily claimed the ball had gone out before Willock's cross.
It was one of a host of debatable moments in a tempestuous encounter at St James' Park.
Arsenal's Kai Havertz and Newcastle's Bruno Guimaraes were both lucky to avoid red cards in the first half.
"The result should not be what it is. Embarrassing what happened, how this goal stands, in the Premier League, this league we say is the best in the world," Arteta said.
"I've been 20 years in this country and now I feel ashamed. It's a disgrace. There's too much at stake here."
Coming just days after they crashed out of the League Cup at West Ham, Arsenal's second successive loss was a painful blow to their title bid.
Arteta's men sit in third place, three points behind leaders Manchester City, with Tottenham able to move into pole position and climb five points ahead of their north London rivals if they beat Chelsea on Monday.
Newcastle's victory capped a memorable week for Eddie Howe's sixth-placed team, who knocked Manchester United out of the League Cup at Old Trafford on Wednesday.
Howe disagreed with Arteta's assessment of the winner, saying: "I haven't seen anything other than what I saw at the time. It looked a good goal to me.
"It's a massive win, full credit to players. It was a battling performance."
In a scrappy first half, perspiration rather than inspiration was the driving force as both teams thudded into tackles and pressed relentlessly.
Much of the frenetic action ended with a lack of focus and composure in the final third and Newcastle failed to muster a single shot in the opening half hour.
Arsenal were hardly more clinical, creating precious little to worry Newcastle keeper Nick Pope.
Reckless Havertz
A tetchy evening finally boiled over when Havertz launched into a reckless challenge that sent Sean Longstaff crashing down, sparking a melee between the teams.
Havertz escaped with a booking from referee Stuart Attwell, much to the frustration of Longstaff and team-mates Gordon and Fabian Schar, who were all booked for protesting the decision.
Gabriel Martinelli's strike was held by Pope in a rare moment of Arsenal incision, but Guimaraes brought an appropriately acrimonious end to the half.
The Brazilian was fortunate to avoid a red card as he elbowed Jorginho in the head, then booted the ball at Havertz and was shoved by Declan Rice in retaliation.
Guimaraes seemed to be embracing his role as the game's agent provocateur and the midfielder's needless barge into Jorginho somehow escaped punishment after the break.
Rice headed narrowly wide after Newcastle failed to properly clear Martinelli's cross.
It proved a costly miss as Newcastle took the lead in controversial fashion after 64 minutes.
When Willock retrieved Jacob Murphy's wayward shot by the corner flag, the ball was perilously close to going out of play.
But the Newcastle midfielder was allowed to continue the attack, whipping over a cross that led to Joelinton's shove on Gabriel, allowing Gordon to finish from barely a yard out.
Arsenal surrounded Attwell to protest but VAR ruled in Newcastle's favour on three counts; deciding the ball did not go out, there was no foul by Joelinton and Gordon was not offside.
Although they dominated possession in the closing stages, Arsenal were impotent in the penalty area as they suffered a first bloody nose this season.