Pelle stormed off straight down the tunnel when he was replaced by Ciro Immobile and completely ignored Ventura's attempted hand-shake.
Italy was trailing 1-0 at the time, but got back in the game with a Daniele De Rossi penalty in the World Cup qualifier.
"These things happen," said Ventura. "I think Graziano was more angry at himself and the way his performance went than anything else."
However, the Italian soccer federation announced on Friday morning that Pelle has been sent back to his club in China, Shandong Luneng, and will therefore miss Sunday's qualifier at Macedonia.
"Manager Giampero Ventura, in agreement with the (Italian federation) FIGC, has decided to exclude Graziano Pelle from the squad for the Macedonia match because of his disrespectful behaviour when he was replaced," a federation statement read.
"To be part of the national team implies the sharing of common values and behaviour conforming to the wearing of the blue shirt, beginning with respect towards the management, players and fans."
Pelle apologised on Instagram for the incident, describing his behavior as "unacceptable".
"I've done something stupid. I behaved unacceptably towards the boss (Ventura) and to my teammates, who have always displayed their values in this fantastic group of which we're part," he posted on Instagram.
"Every serious mistake inevitably has its consequences and it's absolutely right that I take responsibility for what's happened. It's my duty to say I'm sorry."
Veteran Italy goalkeeper Gianluigi Buffon is prepared to forgive and forget the incident.
"He's a great guy and in the cold light of day, I'm sure he will realise he was wrong," he said. "If he apologises for his behaviour, we will be happy to embrace him.
"It was wrong but these things happen in such tense matches."