The Chelsea and England skipper had tried valiently to make the team but failed a fitness test ahead of the match from which England need to avoid defeat to qualify for next summer's tournament.
JT suffered a knee injury in training ahead of England's match in Russia and required surgery.
He is now a major doubt for Saturday's away match against Derby County in the Premiership.
England will be skippered by Steven Gerrard who confirmed Terry's absence.
"I've spoken to John and he is not ready for Wednesday," Gerrard said.
"He is obviously disappointed not to be in the game, but he will still be there and will be a big help to all the players in the dressing room."