The Three Lions found themselves 1-0 in the first half, with the home side being given a penalty in controversial fashion.
Rico Lewis, making his Three Lions debut, jumped for the ball in his side's box and had seemingly cleared the danger.
But VAR then began to review the incident, deeming the 18-year-old Manchester City star to have fouled Aberdeen's Bojan Miovski by putting his hand in his face as he jumped.
After a trip to the monitor, the referee awarded North Macedonia a penalty. Replays show the ball also struck Lewis' hand, but it's not clear what made the spot-kick get awarded.
Jordan Pickford got down to save the initial shot but Enis Bardhi then scored the rebound.
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talkSPORT's co-commentator for the game and ex-England captain Stuart Pearce said: "England are really paying the penalty for not getting after North Macedonia from the first minute."
England fans weren't so sure Lewis should've been punished, though.
"Ludicrous penalty decision. One that is only given because of VAR," one fan wrote on X.
A second added: "Feel so sorry for Rico Lewis. What's he meant to do?"
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Meanwhile, talkSPORT's Adrian Durham said: "VAR is a total joke here... a shambles of a decision."
England were also labelled as 'fortunate' not to concede a penalty for another incident in the first half.
Harry Maguire lost the ball and then pushed Napoli's Elif Elma in the box.
However, the referee wasn't interested, giving England a free-kick as Maguire wagged his fingers at the North Macedonia players asking for a spot-kick.
Gareth Southgate's side did eventually find an equaliser, with second half substitute Harry Kane pressuring Jani Atanasov to concede an own goal to make it 1-1 just before the hour mark.
England already qualified for next summer's European Championships in the last international break after their 3-1 win over Euro 2020 final foes Italy.