Villa manager Dean Smith and defender Tyrone Mings were left furious by referee Jonathan Moss' decision to allow Bernardo's 79th-minute strike despite City midfielder Rodri dispossessing Mings after starting from an offside position.
The Professional Game Match Officials Limited (PGMOL) later clarified their decision, claiming that Mings had deliberately attempted to play the ball and Rodri had therefore not gained an unfair advantage.
But in a statement published on Tuesday afternoon, the Premier League confirmed that new guidance had been added around the offside rule in order to avoid similar incidents in the future.
The Bernardo controversy led the PGMOL to hold dicussions with football's lawmakers, the International Football Association Board (Ifab), and European football's governing body Uefa, which led to a change in guidance.
The new guidance reads: "Where a player in an offside position immediately impacts on an opponent who has deliberately played the ball, the match officials should prioritise challenging an opponent for the ball, and thus the offside offence of 'interfering with an opponent by impacting on the opponent’s ability to play the ball' should be penalised."
The Premier League confirmed that if Rodri had dispossessed Mings with this guidance in place, Bernardo's goal would have been disallowed.
Players standing in an offside position are still able to receive possession from an opponent who makes a deliberate attempt to play the ball if that opponent misplaces their pass or mis-kicks.
Villa benefited from a similar incident in their 2-0 win over Newcastle on Saturday, with Ollie Watkins scoring after receiving the ball from opponent Fabian Schar in an offside position.
However, as Schar deliberately played the ball and Watkins did not impede him in that incident, the Premier League said that that goal would stand under the new guidance.
Smith was shown a red card by Moss following his touchline protests against the decision to allow Bernardo’s goal and served a one-game touchline ban against Newcastle.
"It's farcical. He was 10 yards offside and came back and tackled our player, it's a pathetic law and a pathetic decision," he told BT Sport after an Ilkay Gundogan penalty earned a 2-0 win for City.
"I've not seen a goal like that given. It needs to be looked at. I don't think anyone in this stadium thought it was a goal.
"I thought they would go over to the VAR screen. I saw the incident and saw it was kicking off, so I asked the fourth officials did they get juggling balls for Christmas?
"If that is the law, then definitely [it's a problem]. You can't just have people standing offside and taking advantage of an unfair position."