Blues stars crowded referee Lee Mason at half-time at Stamford Bridge on May 9 as they protested his decision not to allow them to take a corner.
Ref Mason blew his whistle for a corner kick but signalled for half-time before it could be taken.
Captain Cesar Azpilicueta, Cesc Fabregas and Antonio Rudiger led the protests.
Rudiger had to be pulled away by Chelsea coach Carlo Cudicini.
The club were charged with failing to ensure their players "conducted themselves in an orderly fashion" on May 10.
Chelsea were drawing 0-0 going into the break and desperate for a win to keep their Champions League hopes alive.
Laurent Depoitre's second-half strike effectively ended that dream, even with Marcos Alonso's 62nd-minute equaliser.
Defeat at Newcastle on the last day of the season saw Chelsea finish fifth and miss out on Champions League football next season.
Liverpool clinched fourth place behind Tottenham, Manchester United and champions City.
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