Pedri's second-half equaliser was ruled out for an unintentional handball by Ansu Fati after the hour mark and a late Denzel Dumfries handball was not given as a penalty.
Hakan Calhanoglu's goal proved the winner for Inter.
"I am angry and indignant about what we have seen, it is an injustice," Xavi blasted after the game at the San Siro, which complicated Barça's chances of qualification for the last 16.
"I said it on Monday and I have to say it again: the referees have to come out and explain themselves because I don't understand anything.
"He didn't want to give me an explanation after the game. The referees have to speak, I can't speak about a decision I have not given. For me, it's crystal clear. I don't understand...
"I am outraged. I don't understand anything. If Ansu handballs it (involuntarily) but someone else scores, it's a goal. And they disallowed it. And the other one (Dumfries' handball) I do not understand. It's an injustice. The referees have to speak."