With the visiting fans rejoicing, VAR invited referee Anthony Taylor to review the incident on the pitch-side monitor.
Walking past a furious Guardiola, who remonstrated wildly, Taylor ruled the goal out for a foul on Fabinho in the buildup.
City's manager was furious, repeatedly turning to the Anfield fans behind the dugout to gesticulate.
The crowd delighted in his anger and erupted shortly after when Salah fired Liverpool in front.
When Alisson collected an inaccurate free kick from Kevin de Bruyne, the goalkeeper then launched a kick downfield to perfectly pick out his teammate.
This time Salah made no mistake with his finish.
There was still time for more drama when Klopp raced out of his technical area to appeal a decision, leading to him receiving a red card.
Substitute Darwin Nunez might also have doubled Liverpool's lead when making a mess of a late chance with only Ederson to beat.