Palace forward Zaha is accused of improper conduct after a gesture at the travelling supporters was caught on camera.
And Holloway faces the same charge after entering the pitch at the end of a 2-2 draw to confront Leeds' Luke Varney and the match officials.
The Palace manager was angry with referee Dean Whitehouse's failure to send off Varney and team-mate Stephen Warnock for perceived red card offences.
Holloway faces a fine and the possibility of a touchline ban if he fails to overturn the charge, while fourth-placed Palace could be deprived of their star player for one of their remaining nine Championship games.
Zaha was quick to apologise for the gesture on his Twitter page, admitting he had reacted in an "unprofessional" manner to taunts from some Leeds fans.
But there is an FA precedent for punishing his offence - Liverpool's Luis Suarez was banned for one match for a similar reaction at Fulham in December 2011.