The PGMOL confirmed that Stones' goal was ruled out on-field before VAR intervened for a review.
Bernardo Silva was stood in front of Wolves goalkeeper Jose Sa before Stones headed in and was adjudged to be offside by referee Chris Kavanagh.
VAR Stuart Attwell disagreed with the initial decision because Silva moved before Stones connected with the ball and he sent Kavanagh to his monitor, which led to the goal being given.
Only offside was considered in the decision and review. Silva's nudge into Sa was not deemed to have been a foul in play and was not reviewed by VAR.
TrendingAs quoted in the Times, PGMOL said "the offence of holding (ie blocking or obstructing) will be penalised more stringently in set pieces, when an attacker is trying to stop the movement of an opponent" this season.
O'Neil cited the example of Max Kilman having a goal disallowed for Wolves against West Ham in April last season as he highlighted perceived inconsistency with the officiating.
"The reason we were given [for Kilman's goal] was that Tawanda Chirewa was in such close proximity to the goalkeeper that he did have an impact on him. Bernardo Silva is probably less than a yard away from Jose Sa," O'Neil told .
"The same argument could be made, but I am sure they will tell us it was the right call and everyone got it right."
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cookies for this session only. Enable CookiesAllow Cookies OnceO'Neil later said in his press conference: "There's no chance that people are doing things against Wolves on purpose, let's be clear.
"But is there something in the subconscious around decision-making, or without even knowing it, are you more likely to give it to Manchester City than Wolves?"
He added: "If I had to upset someone in a street and there was a little guy and a big guy, I'd upset the little guy. Nothing against little guys, but you know what I mean? Like, there is something in there and they definitely don't do it on purpose.
"I know they're 100 per cent honest and they're doing the best job they can and I respect them fully. But maybe, maybe there's something that just edges in in that direction when it's really tight."
The PGMOL statement read: "Stones' goal was disallowed on-field due to Bernardo Silva being in an offside position and in the goalkeeper's line of vision.
"The VAR deemed Bernardo Silva wasn't in the line of vision and had no impact on the goalkeeper and recommended an on-field review. The referee overturned his original decision and a goal was awarded."
The PGMOL is not commenting on O'Neil's post-match remarks.
Wolves triggered a vote to get rid of VAR in June. Of the 20 Premier League clubs, only Wolves voted to scrap the system.
' Pete Smith:
There are two key elements to Man City's late winner and how the officials have interpreted the passage of play.
First - Is Bernardo Silva offside as he is in the line of sight of goalkeeper Sa? The PGMOL has stated this was the reason the goal was initially ruled out. VAR deemed Bernardo Silva wasn't in Sa's line of sight and advised an on-field review [after the goal was initially disallowed] which ultimately awarded the goal.
The key question: Where was Bernardo Silva when Stones made contact with his header? The answer: Well out of Sa's line of sight.
Secondly - Did Bernardo Silva foul Sa? This is an issue which hasn't been addressed by PGMOL in its subsequent post on X but we have guidance the incident was not judged to be a foul.
"There's a slight nudge that puts the keeper off balance so he's not set [when Stones heads the ball] so I can understand why Wolves will feel aggrieved at this particular moment," said pundit Micah Richards.
"I do believe he's impacted the goalkeeper's ability to save it," added ' Daniel Sturridge.
Wolves boss Gary O'Neil to :
"I managed to remain calm [after the goal was given]. I have been involved in a few of those at Wolves. We've not had many go in our favour. I was expecting the outcome we got.
"There is some grey area there, and some minutiae that you can go either way on that decision. I wasn't too confident that it would go our way.
"Some similarities to our one against West Ham last season. We sent some images to the referee, with clear proof that the West Ham goalkeeper could see the ball.
"The reason we were given was that Tawanda Chirewa was in such close proximity to the goalkeeper that he did have an impact on him. Bernardo Silva is probably less than a yard away from Jose Sa.
"The same argument could be made, but I am sure they will tell us it was the right call and everyone got it right."