The two teams shared the spoils in an enthralling 3-3 draw at the Etihad Stadium on Sunday with Dejan Kulusevski snatching a late point for Spurs.
But the hosts could have wrapped up all three points in the fourth minute of added time after Haaland sent Jack Grealish through to a one-on-one with Guglielmo Vicario.
Haaland had recovered well after being fouled by Emerson Royal, where he got off the grass to clip a delighted lofted through ball over the Spurs back line.
Grealish was the first to the ball, and despite Hooper initially playing the advantage, he inexplicably called the game back to award City a free-kick.
City's players were quick to surround the match official to express their disgust, with Haaland taking to social media in the dressing room immediately after the match.
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Taking to X, he replied to a video of the incident, where he simply stated: "WTF."
His father Alfie then got involved, as he commented: "Terrible."
Pep Guardiola was asked about Hooper's call by Sky Sports, to which he referenced Mikel Arteta's post-match rant after Arsenal's defeat to Newcastle, as he said: "Next question. I will not do a Mikel Arteta comment.
"It is hard when you review the image, the referee decides to blow the whistle after he has already said to play on. After the pass, the whistle, so I do not understand this action.
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The Spaniard added: "It is a pity. Sometimes football is like life, you do not get what you deserve."
Spurs icon Aaron Lennon found the funny side of the decision, as he shared three laughing face emojis, while also saying: "Cheers ref."
Furious Erling Haaland gets into argument with Giovanni Lo Celso as he storms off the pitch following Manchester City's thrilling 3-3 draw with Spurs
The incident proved to be the major talking point on social media, as one football fan messaged: "I've only just seen that refereeing blunder in the City game… genuinely a disgrace."
Another said: "How does the best league in the world have the most incompetent referees in the world?"
A third quipped: "Can we have sin bins for referees?"
Meanwhile one simply stated: "Absolutely atrocious officiating."