The Spain worldwide stood on Long's calf in the first half of Chelsea's 3-2 win over Southampton at St Mary's in the Premier League at the weekend.
But referee Brian Dean missed the accident and Alonso got no form of punishment. The FA confirmed that neither match official saw the incident in real time, but the challenge was caught on video, and the English governing body thus chose to punish Alonso retroactively.
Alonso has until 6 pm tonight to respond to the charges leveled against him.
The incident will now be referred to a panel of three former elite match officials who will review the video footage independently.
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Alonso appeared to stand on the back of Southampton striker Long's calf in the first half as his team trailed 2-0 on Saturday.
The 27-year-old will sit out the next three matches for the west London giants if found guilty - the FA Cup semi-final against the Saints on Saturday, as well as Burnley and Swansea in the Premier League.
"For retrospective action to be taken, and an FA charge to follow, the decision of the panel must be unanimous".
"There is one thing in his mind there, and that is to hurt Shane Long and Mike Dean is looking right at the incident".