The Potters boss was fined £10,000 and warned about his future behaviour after comments made regarding Probert's performance in Stoke's 2-1 Carling Cup loss to Liverpool.
A statement on the club's official website read: "Tony Pulis has today confirmed that he will be appealing against the penalty handed out by the Football Association following a charge of improper conduct."
Pulis himself has expressed his disappointment at the severity of the charge.
"The disappointing and hurtful thing about this judgement is that I have been a manager for almost 800 games and this is the first time I've ever had a charge brought against me," said Pulis.
"I find the severity of the punishment difficult to take in those circumstances."
Stoke face Dynamo Kiev in the Europa League on Thursday night before travelling to Everton in the Premier League on Sunday.