The club is now urging supporters not to engage in the same chant when they face the Blues in the Premier League on Saturday.
And it revealed three supporters had been banned for "a minimum of three years" following February's game at the MKM Stadium.
Three people were arrested for allegedly engaging in homophobic chanting at the match, in which spectators were repeatedly warned to stop the chants over the PA system and messages were displayed on screens.
The chanting was condemned by one fan group as a "stain on our game".
The Football Association later charged the club with failing "to ensure its spectators and/or supporters (and anyone purporting to be supporters) do not use words or behave in an improper, offensive, abusive, indecent or insulting way with a reference - whether express or implied - to sexual orientation" and on Friday announced the club had accepted the charge and received a £30,000 fine.
" condemns, in the strongest possible terms, the offensive and inappropriate language used by the supporters responsible," the club said, saying the "chant in question is recognised as a homophobic slur and its use may constitute a hate crime".
It warned those using the chant faced arrest and criminal charges.
"Ahead of Saturday's trip to Stamford Bridge, the club reminds all supporters that discrimination of any kind is wholly unacceptable and will not be tolerated," it added.
