The Spaniard left Maurizio Sarri absolutely raging on the touchline after refusing to be subbed for the penalty shootout defeat.
With the board raised and Willy Caballero waiting to come on, the £71.6million summer signing remarkably embarrassed the gaffer by overruling his decision.
Sarri completely lost his cool at Arrizabalaga who had gone down twice with cramp towards the end of the contest.
And he has further risked angering the fiery Italian boss even more after winking towards the TV cameras before the penalty shootout.
The Spanish keeper piled the pressure on himself to deliver in the penalty shootout and he had a howler when he failed to keep out Sergio Aguero's tame kick.
He did redeem himself by denying Leroy Sane but David Luiz failed to take advantage and Raheem Sterling won the clash with the winning kick.
The inquest will now begin over how player power prevailed with Sarri also under immense pressure as Chelsea boss.
The Italian manager played down the incident at the full-time whistle and told Sky Sports that it was a "misunderstanding."
He said: "We played a very good match. There was a misunderstanding because on radio I understood there was a problem and the goalkeeper had cramp and not able to go to penalties.
"The goalkeeper said there was no problem and he was right."
When quizzed on whether he would receive any disciplinary action, Sarri responded: "No, now I understand the situation."
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