Balotelli has until 6pm on Wednesday to respond to the charge, which relates to an incident in which he appeared to stamp on Scott Parker's head during Sunday's 3-2 Premier League home win over Tottenham.
However, it is widely anticipated he will accept it, which would trigger a four-match suspension and rule him out of Manchester City's Carling Cup semi-final with Liverpool at Anfield on Wednesday night.
On Tuesday, City assistant manager David Platt said he felt Webb had seen the incident in real time and, therefore, Balotelli should not have been charged.
The player's agent went far further though, accusing Webb of acting like a "coward" and alleging the Yorkshireman changed his mind over the incident once Spurs boss Harry Redknapp has voiced his dismay in the aftermath of his side's defeat, when Balotelli scored the dramatic match-winning penalty in stoppage time.
Bernstein is sufficiently annoyed to issue a strong statement on behalf of the man who refereed the last World Cup final.
"Howard Webb is a fantastic referee and a great ambassador for the sport. His ability and integrity are beyond question," Bernstein said.
"He has the utmost respect from within football in England and around the world. That could not have been demonstrated more clearly than in 2010, when he was chosen to referee the UEFA Champions League final and the FIFA World Cup final, and this summer he has been selected for UEFA Euro 2012.
"We all have a duty to respect our referees. To question their integrity or imply anything other than total impartiality is reckless and unfounded.
"It harms the perception and treatment of referees at every level of football, and we must not allow that climate to exist."
In a press conference on Tuesday, Platt claimed incidents on the field of play often look far worse when they are slowed down.
And Bernstein backed that theory, emphasising Webb only had one look at it.
"Referees have only one live opportunity to make a judgement call on those instances that they see in a fast-paced game," he said.
"They do not have the benefit of numerous camera angles and replays. They make these decisions with honesty and integrity."
It is the comments of Balotelli's agent Mino Raiola that have really irritated Bernstein.
Raiola claimed the Italy striker was feeling persecuted at present and, while the severity of what Balotelli did should not be underestimated, it is easy to see why given team-mate Joleon Lescott escaped punishment for an elbow on Younes Kaboul.
However, the FA added in their own statement: "The FA is only able to take retrospective action where a match official has indicated that they have not seen an incident.
"Specifically relating to the incident involving Mario Balotelli, Howard Webb did not see the incident but on review confirmed he would have sent the player off if he had seen it at the time.
"On review, Webb would not have sent off Joleon Lescott for the incident involving Younes Kaboul.
"The parameters and laws of the game are set by FIFA and not the FA."
