The incident occurred during the second half of last weekend's match at the KC Stadium - which City won 2-0 - when Hart accused Boyd of diving to win a penalty, with the pair going head to head in the ensuing scuffle.
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He will be back in time for the home fixture with Swansea City next month, a week before the club's first FA Cup semi-final appearance for 84 years, against Sheffield United.
An FA statement read: "Hull City’s George Boyd will serve a three-match suspension with immediate effect after an FA charge for spitting was found proven.
"The incident with Manchester City’s Joe Hart, which was not seen by the match officials but caught on video, occurred in or around the 68th minute of the fixture between the two sides on Saturday 15 March 2014.
"Boyd had denied the breach of FA Rule E1(a), but it was found proven at an Independent Regulatory Commission hearing today (Thursday 20 March 2014)."