The incident with the England goalkeeper, which was not seen by the match officials but showed up on television replays, occurred in the second half of Saturday's match at the KC Stadium, which the visitors won 2-0.
Boyd had denied a misconduct charge brought by the FA on Tuesday and mounted an appeal, but that was thrown out at an independent regulatory commission hearing on Thursday.
An FA statement confirmed: "Hull City's George Boyd will serve a three-match suspension with immediate effect after an FA charge for spitting was found proven."
The suspension rules Boyd out of the Tigers' forthcoming Barclays Premier League games against West Brom, West Ham and Stoke.
Television images appeared to show the Scotland international spit in the direction of Hart during the 68th-minute flashpoint, which came with Hull trailing 1-0 to a City side who had earlier been reduced to 10 men following the dismissal of Vincent Kompany.
Boyd, a second-half substitute, went down rather too eagerly under Hart's challenge in the area but his appeals for a penalty were waved away by referee Lee Mason. Hart responded furiously and pushed his head against Boyd as the two exchanged insults.
Hart was booked by Mason and as a result was subject to no further action, although Boyd later insisted that Hart was lucky to stay on the pitch, claiming: "He didn't nut me but he's put his head in, so he should have got sent off really."
The loss of Boyd ahead of three crucial fixtures will come as a blow to Tigers boss Steve Bruce, who launched an impassioned defence of his player after Saturday's match, saying: "George Boyd would not do that, not a chance - not deliberately, anyway. He is as honest as they come."
Bruce must now have to do without a player that he frequently employs off the bench, with 19 of Boyd's 25 league appearances this term coming as a substitute.
Hull, who despite an impressive first season back in the Premier League are just five points above the relegation zone, are already without winger Robbie Brady and defenders Paul McShane and Joe Dudgeon as the business end of the season approaches.