The 78 year old is currently in Barbados where it is expected he will remain as he serves his six week suspension from football activities.
In their ruling the FA were keen to stress that they do not believe Whelan to be racist and that the punishment is a reflection of the comments taken objectively.
Whelan is allowed to appeal the punishment but it is thought he will accept the judgement.
The chairman had previously announced that he would resign if found guilty of being a racist which the FA were keen to point in their ruling is not the case.
A statement on the club's official website read: "Wigan Athletic can confirm the findings of an independent regulatory commission following statements made by Chairman Dave Whelan in the Guardian newspaper on November 20.
"In summary, the FA Commission concluded that: 'We are satisfied on the evidence before us that Mr Whelan is not a racist. We are equally satisfied on the evidence before us that Mr Whelan did not intend to cause any offence by his comments. It is clear that he himself is very upset by the words he used and he moved very quickly to apologise publicly, plead guilty and begin to make amends'."
With the ongoing charges over manager Malky Mackay the club will be keen to put this behind them and get back to football, starting with Saturday's trip to face Bolton in the FA Cup Third Round.