The incident occurred when the 27-year-old Northern Ireland international tangled with Cisse in the 38th minute of United's 1-0 Premier League victory at St James' Park on Wednesday.
"Manchester United's Jonny Evans denies FA charge in relation to incident involving Papiss Cisse," the FA said on Twitter.
"Independent Regulatory Commission hearing tonight (Friday), decision expected tomorrow (Saturday)."
Senegalese international Cisse, 29, faces a heavy punishment, according to media reports, after he accepted the FA's charge on Thursday.
(Reporting By Tom Hayward, editing by Pritha Sarkar)
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