The Serbia international shoved Ashley Barnes to the ground during the 1-1 draw, but was on the receiving end of a horrific tackle from the Burnley striker beforehand - a challenge labelled "criminal" by Blues boss Jose Mourinho.
Chelsea subsequently appealed the decision in a bid to have the red card rescinded, but the FA have only decided to reduce the ban to two games - thus ruling him out of the League Cup final against Tottenham and the Premier League clash with West Ham.
“In reaching this decision the members of the Regulatory Commission rejected the mitigation advanced by Nemanja Matic in respect of the provocation and tackle he received which led to his act of violent conduct," said Roger Burden, chairman of the FA's regulatory commission, in a statement.
"The violent response of Mr. Matic to the nature of the tackle cannot be condoned and does not vindicate his subsequent actions. The members of the Commission did, however, accept the mitigation in respect of the level of force used by Mr. Matic and the nature of the contact he made with Mr. Barnes of Burnley FC.
"Having made those considerations we determined that the standard punishment of a three-match suspension would be clearly excessive and, therefore, ordered that the suspension be reduced to two matches.”
However, Chelsea have expressed their frustration at the decision, and claim that Matic has been "unjustly punished" for his reaction to a "career-threatening tackle", and also maintain that the affair is evidence that referees need to do more to protect players from such challenges.
"The Chelsea Football Club board is extremely disappointed and frustrated that the FA Regulatory Commission has today decided not to reduce Nemanja Matic’s suspension to the maximum extent permitted under FA rules," read a statement.
"Chelsea FC challenged the standard three-match suspension which automatically followed the red card issued to Matic by referee Martin Atkinson during Saturday’s Premier League match against Burnley.
"There has been universal condemnation of the reckless challenge made by Ashley Barnes on Matic and it is the club’s view that he has been unjustly punished with a two-match ban for his reaction to a career-threatening tackle.
"It is Chelsea’s opinion that referees and the football authorities must do more to protect players at all levels of the game from dangerous challenges. This decision also clearly demonstrates a need for consistency and fairness in the disciplinary process."