The Portuguese missed the match at home to Chelsea after the FA found Silva guilty of an aggravated breach of rules because his tweet included a reference "whether expressed or implied, to race and/or colour and/or ethnic origin".
Silva tweeted an image of a young Mendy alongside an image of the character representing the Spanish chocolate peanut brand Conguitos in September, deleting it shortly afterwards.
The player said that it was meant as a joke between friends, but he has still been banned, fined 50,000 and must complete face-to-face education as part of his punishment.
However Guardiola, who has stood by the 25-year-old, believes the FA are trying to make an example of Silva.
"In this situation, the less important thing is the fact that we missed him. He has been accused of something he's not," said the City boss.