Warnock appeared to infer that referee Craig Pawson was using double standards by not booking John Terry yet cautioning a Palace player for a similar offence.
The FA said in a statement: "It is alleged that Warnock's post-match comments constituted improper conduct in that they implied the match referee was motivated by bias; and/or brought the game into disrepute, in contravention of FA Rule E3[1]."
Warnock has until 6pm on Monday to respond to the charge.
Meanwhile, the FA has contacted Swansea manager Garry Monk to seek his observations about his post-match comments following the defeat at Stoke.
Monk blasted match official Michael Oliver for a "disgusting" decision in awarding a penalty for a foul on Stoke's Victor Moses, and made vitriolic criticism of Moses for what he claimed was a blatant dive.
Warnock is no stranger to FA charges for criticism of referees
His latest charge comes after the Palace manager suggested referee Pawson may have looking to "even up" his decisions after showing the red card to Chelsea's Cesar Azpilicueta - two minutes later he sent off Damien Delaney.
He told reporters after the match: "They buzzed me down from upstairs saying it'll be evened up if we're not careful
Delaney shouldn't have given him a chance, but it was wrong that four or five Chelsea players surrounded the referee.
"I thought he was influenced by one or two things
John Terry's (non) booking - if that's one of my players, it's a booking
I don't understand why it's not an even platform."
Source : PA
Source: PA