Pardew shoved the official during his side's Barclays Premier League win over Tottenham on Saturday.
The Magpies boss apologised unreservedly after the match but it has not prevented the FA acting and he now has until 4pm on Thursday to respond to the charge.
Given Pardew's comments after the match, it seems unlikely he will contest it. He said: "It was ridiculous and I apologised publicly. He was right in front of me and I thought the ball was out and I shoved him.
"I went to see him and told him it was stupid and I don't know what I was thinking."
Pardew reacted angrily having thought the official had missed a throw-in for his side moments before Spurs shot narrowly wide.
The incident was missed by referee Martin Atkinson but it was immediately brought to his attention by fourth official Lee Mason.
Pardew was ordered to watch the final 20 minutes of the match at Sports Direct Arena from the stands.