Robin van Persie's last gasp free-kick snatched a 3-2 win for United over their close neighbours and Barry's frustrations appear to have boiled over following the final whistle.
The England midfielder will receive a one-match ban if he does not contest the charge by 4pm on Thursday, while an extra game would be added to the suspension if he loses an appeal against the charge.
An FA statement read: "Manchester City's Gareth Barry has been charged by The FA for a breach of its Rule E3 in that he used abusive and/or insulting words towards a match official following the Manchester City v Manchester United game on Sunday 9 December 2012."
The match had already been marred by ugly scenes with United defender Rio Ferdinand being struck by a coin as he celebrated Van Persie's winner.
City have also removed a season ticket from supporter Matthew Stott, who was restrained by the hosts' goalkeeper Joe Hart after he ran onto the pitch to confront Ferdinand.
Police charged eight other people, including for a racially aggravated public order offence, pitch encroachment, breach of football banning orders and other public offences.
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