The incident occurred during United's 1-0 Premier League win over Newcastle at St James' Park on Wednesday.
Evans has denied spitting at Cisse, but the Newcastle striker has issued a public apology for his behaviour. Both players could face six-game bans if the charges against them are proven.
"Newcastle United's Papiss Cisse and Manchester United's Jonny Evans have both been charged by The FA following their game on Wednesday 4 March 2015," the FA said in a statement on its website.
Cisse quickly accepted the FA charge, with Newcastle managing director Lee Charnley saying: "Both ourselves and Papiss agree that this kind of behaviour is not acceptable.
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"In life, when you do something wrong you have to front up, admit your mistakes and accept the punishment.
"Papiss was proactive this morning in making a full and heartfelt apology, which he did in advance of any notification from the FA regarding this charge."
As the pair climbed to their feet, Evans seemed to spit towards the ground and Cisse appeared to react by spitting at the United defender's neck.
Referee Anthony Taylor did not take action against either player, but footage of the incident was reviewed by a three-man panel of former elite referees, who all agreed that both players should have been sent off.