The Blues were angered when Lee Mason awarded the hosts a corner but then blew for half-time before it was taken by Willian. The official had adjudged the required stoppage time had elapsed.
Captain Cesar Azpilicueta, midfielder Cesc Fabregas and defender Antonio Rudiger led the protests. Rudiger had to be dragged away by assistant coach Carlo Cudicini, who also addressed Mason.
"Chelsea have been fined £20,000 after accepting a charge for failing to ensure their players and/or officials conducted themselves in an orderly fashion," an FA statement said.
The Blues criticised Huddersfield for time-wasting during the game, the result of which hit their hopes of qualifying for the Champions League next season.
A 3-0 loss at Newcastle on Sunday ensured Chelsea finished fifth but Antonio Conte's side could yet end the season with a trophy if they win Saturday's FA Cup final against Manchester United.