The 70-year-old described Premier League officials as "the worst" in the world following the loss on March 31 and faces punishment relating to remarks he made to three broadcasters. He has until April 16 to respond.
Warnock felt aggrieved after Cesar Azpilicueta's 84th-minute equaliser was allowed to stand despite the Chelsea defender being in an offside position.
The Cardiff boss also felt his team had two penalty claims rejected by referee Craig Pawson and that Antonio Rudiger should have been dismissed for a challenge on Kenneth Zohore.
Warnock avoided punishment for staring down Pawson and his fellow officials at the end of the game, which Chelsea won late on through a Ruben Loftus-Cheek header, but could yet be sanctioned for his post-match comments.
An FA statement read: "Neil Warnock has been charged with three breaches of FA Rule E3.
"It is alleged that comments he made in a post-match interview with the BBC, and a post-match interview with Sky Sports, following the Premier League game against Chelsea on 31 March 2019, were improper in that they questioned the integrity of the Match Official and/or implied bias.
"It is further alleged that comments he made in a TalkSport Radio interview on 01 April 2019 constitute improper conduct and/or bring the game into disrepute."
Cardiff have a crunch Premier League fixture next as they travel to Burnley, hoping to pick up what would be a vital three points in the fight for Premier League survival.
However, the dropped points against Chelsea have left them in a precarious position, sitting 18th with 28 points - five off safety, with a significantly poorer goal-difference than Southampton and Brighton - the two teams above them on 33 points.
The Bluebirds have still got to host Liverpool and visit Old Trafford on the last day, but crunch fixtures against Brighton and already-relegated Fulham represent huge opportunities for the club to claw their way out of the drop zone.