Mourinho was accused of making "abusive and/or insulting and/or improper" remarks to a television camera after his side's dramatic 3-2 win at Old Trafford on October 6.
The Commission ruled against the FA, deciding that the context of the comment was important, and that the FA expert had failed to prove that the words Mourinho used were in themselves were abusive, insulting or improper.
Having expressed surprise at the verdict, the FA have now, as expected, chose to appeal after "carefully considering" the commission's written findings released on Wednesday, which again raises the possibility of Mourinho receiving a touchline ban.
"Having carefully considered the written reasons of the independent regulatory commission relating to the case involving Jose Mourinho, the FA can confirm it is appealing the decision, it said in a statement".
To support his case, Mourinho also produced a list of examples where managers and players have sworn during matches and not faced FA charges.
To support his argument, Mourinho hired an expert called Simao Valente, who is described as "an Assistant Professor at the University of Lisbon and an expert in the Portuguese language, including colloquialism". Thus, the objective person would have had to lip read JM's mouth and interpret Portuguese colloquialisms to accurately decipher the comments.
"Do you understand Italian?" said Mourinho.
Valente then argued that it was important to pay heed to the context within which the phrase was said.
So lost has the 29-year-old looked that he is generating more transfer talk 12 months on from his deal with the Red Devils, with Jose Mourinho struggling to bring the best out of him.
They asked Pedro Xavier, who is described as "an expert in the translation and interpretation of lip reading of colloquial Portuguese language" to study the clip of Mourinho and to offer an interpretation of the words said.
Valente interpreted the repeated phrase as "vao levar no cu, filhos da puta", which he translated to mean "go take it in the a***, sons of the w****" in the literal sense, and "f*** off you sons of b******" or "f*** off you a*******" as an idiomatic translation.