The Gunners thought they had levelled the match in the closing minutes at Villa Park when Havertz crept in at the back-post and turned the ball into the net.
However, the German was quickly denied what would have been a huge goal in the Premier League title race when Australian referee Jarred Gillett blew his whistle to disallow the goal.
Confusion quickly reverberated around Arsenal’s ranks with Mikel Arteta’s side believing they had snatched a point at one of the toughest grounds in the English top-flight before having the goal cancelled out.
VAR scrutinised the decision with Michael Salisbury and assistant Scott Ledger spanning over every angle of the incident that saw the ball rattle between Havertz and defender Matty Cash.
Replays showed Havertz had controlled the dropping ball with the top of his hand before smashing his shot into the back of the net.
The VAR duo eventually agreed with Gillett’s initial on-field decision and play eventually resumed after Villa goalkeeper Emi Martinez received treatment for an eye injury.
Villa were able to navigate their way through a tricky final few minutes and hold onto their narrow lead to claim another massive win, having already beaten Man City earlier in the week.
Former Liverpool defender Jamie Carragher praised Gillett for making an ‘unbelievable’ decision that was later confirmed to have been the correct call by VAR.
Commentating on the match for Sky Sports, Carragher said: ‘It comes off the top of his hand and then he puts it in just there before he volleys it in.
‘That is an unbelievable decision from the referee if he’s given that in real-time,’ he added.
Arsenal attempted to rally after their goal was chalked out but couldn’t manage an effort on target with Eddie Nketiah blazing a header over the bar.
Defeat ensures Liverpool keep their place at the top of the Premier League, with Unai Emery’s Villa now just one-point behind the Gunners.