Former Palace forward James Vaughan netted the only goal of the game as the Tykes edged a fiery encounter at the John Smith's Stadium - and a post-match scuffle followed.
The Huddersfield website said: "Huddersfield Town can confirm it has been charged by the Football Association following Wednesday night's win over Crystal Palace.
"The Club has been charged on FA Rule E20(a) - failure to ensure that its players/officials conducted themselves in an orderly fashion.
"Visitors Crystal Palace have also been charged with the same offence. Huddersfield Town is considering its response and has until 4pm on 6 February to respond to the charge."