Balotelli's agent Mino Raiola said the striker feared he was being victimised by English referees following the City forward's violent conduct charge for stamping on Tottenham midfielder Scott Parker on Sunday.
Raiola said on Tuesday that Webb -- who refereed the 2010 World Cup final -- had acted like "a coward" by reporting Balotelli retrospectively in his match report sent to FA chiefs.
Raiola accused Webb of being influenced by post-match comments by Spurs boss Harry Redknapp, who had fumed about the incident following the 3-2 defeat.
However, Bernstein sprang to Webb's defence on Wednesday.
"Howard Webb is a fantastic referee and a great ambassador for the sport. His ability and integrity are beyond question," Bernstein said in a statement.
"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."
Manchester City have until 1800 GMT on Wednesday to decide whether or not they plan to appeal Balotelli's charge.