"We wanted him to know that the vast majority of Forest fans are fair-minded individuals and that small minority who took it upon themselves to abuse him and are not representative of our support."
As previously reported Jones was subjected to vile abuse from the home fans.
Now the FA are to investigate
"We strongly condemn any chanting which contains foul and abusive language or is of a homophobic or discriminatory nature.", said an FA statement.
"At this stage is that we are gathering information on this."
League Managers Association vice-chairman Frank Clark, a former Forest manager and player, was at the game and heard the barrage of verbal abuse aimed at Jones.
He said: "Football must make a stance against it.
"The FA are promoting their Respect campaign and there is some abuse from crowd that is totally unacceptable.
"It is only a small minority of the crowd but that doesn't make it any less despicable, there was no cause for it at all and totally beyond the pale.
"A lot of abuse from spectators towards managers, and players for that matter, is well over the top and has no place in the game.
"As a manager you accept you are going to accept stick from opposing fans, and sometimes your own, but this kind of thing goes far too far."