Terry, 31, said in court he was repeating what he thought Ferdinand had said to him as they traded insults.
But the lower burden of proof in FA cases means that both Terry and Ferdinand could be sanctioned.
The FA said it "notes the decision in the John Terry case and will now seek to conclude its own enquiries".
Ferdinand also admitted in court that he had used insulting words towards Terry during the altercation at Loftus Road last October.
The governing body suspended its investigation surrounding the incident in November, when it became apparent that the case would go to court.
Garth Crooks, of anti-racism in football campaign Kick It Out, says it is only half-time for John Terry
"Terry has not been charged under law but it doesn't mean he will not be charged under FA rules," said Kick it Out ambassador Garth Crooks.
"So for John Terry I'm afraid that this is only half-time."
Crooks added: "What we are talking about is the language that was used by a particular player and the question for the FA now is: is that acceptable for a professional footballer?"
In his summation of the case at Westminster Magistrates' Court, Judge Howard Riddle said that "there is no dispute that John Terry directed [racially sensitive] words in the direction of [QPR defender] Anton Ferdinand".
But in reaching a not guilty verdict, he stated it was "possible that what was said was not intended as an insult but rather as a challenge to what he believed had been said to him".
The prosecution had to prove beyond reasonable doubt that Terry had used the words in an insulting manner, which it could not.
But the FA can seek to charge England defender Terry on the balance of probabilities.
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