Holloway's behaviour after the 1-0 home defeat by Tottenham Hotspur in the Premier League at Selhurst Park amounted to improper conduct, the Football Association said in a statement on Tuesday.
His allegations of biased refereeing in post-match comments had also brought the game into disrepute. He has until 1500 GMT on Friday to respond to both charges.
Holloway, speaking on Sky Sports, called into question referee Mark Clattenburg's decision to award Spurs a penalty for an accidental handball by defender Dean Moxey seconds after his team were denied a blatant foul on Stephen Dobbie.
He said lesser teams suffered from decisions that generally go the way of more illustrious opponents, something he also experienced at former club Blackpool.
"It's going to be a long, hard season for me with these people (referees). I had this with Blackpool - certain clubs get fouls and others don't," Holloway said.
"I just want a bit of fairness. I want a foul like anyone else would have got one. I've got a horrible taste in my mouth after that."
The game with Spurs was the first in the league this season for promoted Palace.
(Reporting by Rex Gowar; editing by Tony Jimenez)
