The 63-year-old has been charged with an alleged breach of Rule E3 and has until 4pm on Friday to respond.
Leeds forward Luke Varney was sent off early in the second half at The Den for an elbow on Adam Smith before Chris Wood headed home a winner for the hosts five minutes from time.
Warnock was furious with referee Mark Halsey over the red card.
A statement on the FA's website read: "Leeds United manager Neil Warnock has been charged by the FA for an alleged breach of Rule E3.
"The charge is in relation to improper conduct following his side's game at
Millwall on November 18, 2012."
Warnock said after the match: "I thought we were very short-changed. I thought we did all right in the circumstances - we tried to win the game.
"Referees aren't as consistent - they've gone backwards, I think. I didn't think someone of Mark Halsey's quality and experience would have gone straight for his red card, and I think he'll be disappointed when he sees it, but that will do us no good."