The Italian gaffer wanted to bring his No1 off the field after he went down with cramp just minutes before the shootout and ultimately Chelsea's cup final defeat.
With penalty specialist Willy Caballero ready to come on and the board raised, Arrizabalaga sensationally refused to budge.
Sarri was growing incensed on the touchline and continued to demand that the £71.6million keeper should be subbed for the shootout.
Caballero was the hero three years ago when he saved three penalties as Man City lifted the League Cup.
Even assistant boss Gianfranco Zola did his best to convince Arrizabalaga to come off pitch.
But he continued to stand his ground and player power would prevail as a furious Sarri failed to contain his emotions on the touchline.
Sarri launched an item to the ground and looked to be heading towards the Wembley exit before eventually coming back to the dugout.
It is a new embarrassment for the under-pressure manager who will feel he has been undermined by his player.
Arrizabalaga remained in goal for the penalties and blundered Sergio Aguero's spot-kick – allowing it to slip under his arm.
But he somewhat redeemed himself by saving Leroy Sane's before David Luiz failed to take advantage and hit the post.
Raheem Sterling scored the winning penalty as the Spanish keeper trudged his way off the field.
But the inquest will now begin over why the stopper refused to follow his manager's instructions.
Chelsea fans had little sympathy for their "disgraceful" keeper with the majority claiming he was in the wrong.
His Wikipedia page was changed several times in the aftermath as he was targeted by trolls.
One said: "Kepa should be dropped and fined. You can't disrespect your manager in a game like this."
Another added: "Kepa should never play for Chelsea again.
"If the players start refusing to be substituted, thereby humiliating the manager, they make the club look ridiculous too.
A Chelsea fan page commented: "One thing for sure if Kepa will pay for this."
However, Sarri claimed Kepa was RIGHT to ignore his orders, but simply went about it in the wrong way.
And he plans on hauling him in for talks
Sarri said: "I was really angry.
"I understood he had cramp, so I didn't want the goalkeeper to go to the penalties in that physical condition. I realise the situation after three or four minutes when the doctor arrived on the bench.
“I wanted Caballero on the pitch, but the goalkeeper wanted to let me know he was in condition to go to the penalties. It was only a big misunderstanding.
“Kepa was right, but in the wrong way. Wrong in the way he conducted himself, but mentally he was right because he was able to go to the penalties. But I realised everything only when the doctor arrived on the bench. Not before.
“I want to talk with him because he needs to understand that, for a misunderstanding, we can go in trouble. So I think I have only to explain exactly the situation to Kepa. Without any other problem.
“Kepa only said: 'No, no, I'm very well and able to continue.' He understood I wanted to change for an injury. He was only telling me his word, saying he was really very well. So I think that, in 120 minutes, a discussion can happen with the players.
“I think we have to concentrate on football. Of course I will speak to him. As I said before, he was right for his motivation. But not for the conduct.”
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