Now he will have to rest up for a further two weeks, after seeing a specialist, before a further assessment is made.
Villa will meet Manchester United in the final at Wembley on February 28 - barely a week after Warnock is checked out again.
Warnock has played a key role in a revamped back four alongside James Collins and Richard Dunne in helping Villa challenge for a Champions League spot since his £7million move from Blackburn during the summer.
He has also emerged as a candidate to be the number two left-back to Ashley Cole in Fabio Capello's World Cup squad.
Villa boss Martin O'Neill said: "Stephen will have to rest for a while. We will have a look and see how he is in a couple of weeks. That is what the specialist has said.
"We will have to see if it will settle down. Obviously, he's desperate to be playing. It's disappointing because he's been brilliant for us.
"Stephen, James Collins and Richard Dunne have given us an enormous boost.
"Their ability, their character - everything about them - has been excellent.
"They love to play and they've also built up a really decent understanding. Taking all that into consideration it (Warnock's injury) is a blow.
"Obviously it is worrying for Stephen and he has done so much to get us there to the cup final. It would be devastating if he missed that."
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