Niasse went down inside the Crystal Palace box on Saturday, with referee Anthony Taylor deeming the Senegal international had been fouled by Eagles defender Scott Dann.
Dann himself reacted angrily over the decision, saying Niasse had "conned the referee". Leighton Baines tucked away the resulting penalty to cancel out Wifried Zaha's early opener at Selhurst Park.
"Everton's Oumar Niasse has been charged for 'Successful Deception of a Match Official' following the game against Crystal Palace on 18 November 2017," said a statement on the Football Association's website.
Niasse could become the first Premier League player to be hit with a retrospective ban for diving following the introduction of the new law at the start of the season.
But the 27-year-old Senegalese player will only be handed a two-match suspension if the panel that convenes to oversee his case unanimously agree that Niasse was guilty of the offence.
"It is alleged he committed an act of simulation which led to a penalty being awarded in the 5th minute of the game," the FA statement said.
"He has until 6:00 pm (1800 GMT) on 21 November 2017 to respond.
"Incidents which suggest a match official has been deceived by an act of simulation are referred to a panel consisting of one ex-match official, one ex-manager and one ex-player.
"Each panel member will be asked to review all available video footage independently of one another to determine whether they consider it was an offence of 'successful deception of a match official'."
Niasse, who himself scored later in the 2-2 draw, defended himself following the incident and told the Liverpool Echo he would be "shocked" to be charged.
The forward was out of favour at the start of the campaign but, with the Toffees struggling for results, he has now scored five goals in seven Premier League appearances this season.