In a statement
, English football's governing body said the players had been charged "in relation to an alleged breach of FA Rule E1[a] in that in or around the 38th minute of the game the two players spat at each other.
The players have until 6pm GMT on Friday to respond to the charge, and could face six-game bans if found guilty.
Both Evans and Cisse released statements the day after the incident, with Evans saying
: "I would like to make it clear that I did not spit at Papiss Cisse."
Cisse's statement said
: "I reacted to something I found very unpleasant. Sometimes it is hard not to react, particularly in the heat of the moment. I have always tried hard to be positive a role model, especially for our young fans, and yesterday I let you down."
Spitting at another player is considered beyond the pale by professional footballers, and former Liverpool midfielder Dietmar Hamann, now a TV pundit, told the BBC's Match of the Day programme the incident had been "disgusting."
"This is not acceptable," he said. "There are kids watching. Something has to be done. The behaviour towards each other and the referee is deteriorating on a weekly basis."
Ex-Manchester United midfielder Paul Scholes said he did not believe Evans had deliberately spat at Cisse, telling BT Sport: "Look, it's not very nice. I think Jonny is spitting on the floor.
"I know Jonny -- he's not that type of person. If he wants to do that then it's not hard to miss, is it? He's only stood a yard away from him. What Cisse does afterwards is unforgivable."
And former Liverpool player Steve McManaman told the channel: "Cisse stands up and spits right at Jonny Evans' neck from about six inches. It's absolutely disgusting.
"Two wrongs do not make a right. If Jonny Evans has spat at him then it's wrong, but for Papiss Cisse to get up and react like that is absolutely disgusting. We talk about bad tackles, but that is worse."