The Football Association's independent regulatory commission partially upheld an appeal lodged by Chelsea on Tuesday.
Matic, 26, was sent off in Saturday's 1-1 draw with Burnley after reacting to a high tackle from Ashley Barnes.
In a statement, Chelsea said they were "extremely disappointed and frustrated" that Matic must still serve a ban.
Matic will miss the League Cup final against Tottenham Hotspur at Wembley and next week's league match at West Ham United, on Wednesday 4 March.
A statement on Chelsea's website, published under the headline 'Chelsea FC appalled with the FA's decision on Matic', said the board was unhappy that the commission decided against reducing the ban by the "maximum extent permitted under FA rules".
The commission could have reduced the ban to one game, but could not overturn the red card.
The Chelsea statement added: "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."
The Serbia midfielder pushed Barnes to the ground after the Clarets forward caught him on the shin.
Blues boss Jose Mourinho defended Matic's reaction and described the tackle from Barnes as "criminal", while Match of the Day pundit Alan Shearer said the challenge was "horrific" and "dangerous".
However, Burnley manager Sean Dyche said that while slow-motion replays made the incident look "ugly", the challenge was merely a "coming together at an unusual angle".
Roger Burden, chairman of the FA's regulatory commission, said the panel had "rejected the mitigation advanced by Nemanja Matic in respect of the provocation and tackle he received which led to his act of violent conduct".
He added: "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."
Chelsea's statement added that they would await the FA's written reasons before commenting further, and said "referees and the football authorities must do more to protect players at all levels of the game from dangerous challenges".
Chelsea midfielder Nemanja Matic's violent conduct ban has been reduced from three games to two, but he will still miss Sunday's League Cup final.