Wilder was upset with decisions during the 3-2 loss and his post-match comments intimated that officials were more likely to give decisions against the Yorkshire club.
He also accused a referee's assistant of being disrespectful for continuing to eat a sandwich while Wilder tried to talk to referee Tony Harrington after the game.
Wilder was charged with a breach of Rule E3.1 in relation to his post-match comments that the FA alleged constituted 'improper conduct in that they implied bias/or attacked the integrity of the referee, or referees generally and/or bring the game into disrepute'.
An FA statement said Wilder had accepted his charge and that an independent regulatory commission had imposed the fine.
Wilder's anger was sparked after his goalkeeper Ivo Grbic was forced off with concussion after a collision with Palace's Jean-Philippe Mateta who did not receive a yellow card.
"It's yet another ridiculous performance from the referee. I was told by a Premier League referee, who's as honest as the day is long, 'Get ready, because every tight decision will go against you, every 50-50 will go against you'", Wilder said in his post-match press conference.
"Every tight decision goes against us. I'm not looking back over the last ten games, it's over a longer period, before I was here as well. Maybe the thought process is that, 'They won't be long in this division and I might be refereeing the other team next year, so I don't want to upset too many people.'"
Sheffield United are bottom of the league standings with 13 points from 25 games.
