Terry had been facing a three-match ban after referee Mark Halsey deemed the tackle on City striker Jo to be serious foul play.
But Chelsea appealed successfully, prompting Ferguson to claim that referees' chief Keith Hackett had told Halsey to overturn the card.
That decision clearly upset Ferguson, who will be without Nemanja Vidic for the same game after the Serbian defender was sent off against Liverpool on Saturday.
"If it had been a Manchester United player Hackett would never have done this for us," he said.
The FA vehemently denied his allegation and is looking into his comments.
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