The midfielder, who has already served a mandatory one-match suspension for his red card at Old Trafford almost two weeks ago, admitted a Football Association charge of improper conduct levied for his angry refusal to leave the field, but the club still intend to appeal the additional ban.
A spokesman told the club's website: "We have put in the appeal and requested that the penalty not be set aside pending the outcome. Consequently, Javier is suspended for Saturday's game at Arsenal."
Mascherano picked up an automatic one-match suspension for the red card and a ban for a further two Premier League games as well as a £15,000 fine.
He admitted a charge of improper conduct after a personal hearing and was punished further by the FA, with the additional suspension meaning he would miss tomorrow's trip to Arsenal and the home game with Blackburn on April 13.
But Liverpool have confirmed they are unhappy with the "inconsistency of sentencing based on past precedents", with Mascherano seemingly being made a scapegoat for some high-profile displays of petulance towards referees.
Those precedents could include the cases of Arsenal striker Emmanuel Adebayor, who staged a long protest after being sent off in last season's Carling Cup final, and that of Watford's John Eustace, who showed a reluctance to leave the field after being dismissed last month.
Both players had their automatic bans extended by only one match and Liverpool's decision not to "set aside" the impeding suspension against Arsenal would suggest they are hoping for a reduction to one match.
Mascherano, meanwhile, has expressed his regret for the incident and publicly apologised.