The 'Blues' overturned a two-goal deficit at the weekend to secure a 3-2 victory in the space of ten minutes but the biggest talking point from the game was Alonso's horror tackle on the opposing striker.
Following the defeat, Southampton manager Mark Hughes accused the defender of trying to break Long's leg, which happened when Chelsea were 1-0 down.
Match referee Mike Dean did not give Alonso a yellow card for the challenge, which will allow the FA to take retrospective action over the incident after all officials confirmed that they had not seen the incident.
It will now be referred to a panel of three former elite referees, who will review the video footage independently. For retrospective action to be taken, the decision of the panel must be unanimous.
Depending on what punishment is dished out, Alonso could miss Chelsea's FA Cup clash with Southampton at the weekend as well as league fixtures against Burnley and Swansea if handed a three-match ban.
Alonso has until 6pm on Wednesday to respond to the charge.