Silva has been charged by the Football Association (FA) after likening a picture of a young Mendy to the mascot of Spanish confectionery company Conguitos.
The likes of Pep Guardiola, Raheem Sterling and Tiemoue Bakayoko have offered support to the Portugal international, who faces a possible six-match ban if found guilty of racist behaviour by the FA.
Benfica, with whom Silva started his career before moving to Monaco in 2014, initially on loan, have hit out at suggestions that the 25-year-old could be in any way racist.
"Bernardo Silva is a young man who always been distinguished for his simplicity, his character and his good upbringing," Benfica stated in their weekly newsletter, published on the club's official website.
"Wherever he goes, he is always missed and always ensures that the managers and team-mates who deal with him are unanimous in complimenting his happy and spontaneous nature. In Benfica, we are enormously proud of you, Bernardo!
"Turning a simple joke between two team-mates and friends into a tweet with racist intent and opening a misconduct charge demonstrates and signals a disease of our times."
Silva has until October 9 to respond to the FA's charge.
A statement on the FA's official website read: "Bernardo Silva has been charged with misconduct for a breach of FA Rule E3 in relation to a social media post on 22 September 2019.
"It is alleged that the Manchester City player’s activity breaches FA Rule E3(1) as it was insulting and/or improper and/or brought the game into disrepute.
"It is further alleged that the activity constitutes an 'Aggravated Breach', which is defined in FA Rule E3(2), as it included reference, whether expressed or implied, to race and/or colour and/or ethnic origin."
Should Silva accept the charge, he could face a ban and a fine, while a failed appeal could result in a longer suspension and a higher financial penalty.
Manchester City take on Wolves in Premier League action on Sunday.