Terry was suspended for four games and fined £220,000 by an independent Football Association regulatory commission after he was found guilty of racially abusing QPR defender Ferdinand in a game last season.
On Thursday he chose not to appeal against the punishment and apologised for using offensive language.
However, many feel that the punishment was inadequate and it is reported that Ferdinand and his brother Rio will join Reading striker Jason Roberts in refusing to wear a 'Kick It Out' t-shirt for the equality group's annual week of action in protest.
Bernstein says the Terry case has had widespread implications but is hopeful that the damage can be repaired.
"The decision by John Terry not to appeal his FA charge hopefully brings to a close a difficult period for the domestic game in England in which, unfortunately, the reputation of English football has been damaged," Bernstein said.
"It is a shame that one high profile incident has had such a major impact. But this single event should not be allowed to overshadow the massive strides taken by players, managers, clubs, leagues and so many across the national game in terms of equality and inclusion.
"The damage of this affair is not irreparable, but as events this week have shown there are still many lessons to be learnt in the wider fight against racial abuse and discrimination of all types."
The time taken for the FA to handle the case has been criticised, although their investigation was held up by the need to defer to the police and the Crown Prosecution Service's criminal proceedings.
Bernstein continued: "John Terry has now been sanctioned and held accountable for his actions. I am pleased he has apologised and we must now draw a line under this matter.
"We too will learn from the case. We have noted criticisms made by the independent regulatory commission as to how matters could and should be improved. I will ensure any lessons that arise from the ruling will be learnt quickly and appropriately."
England's Under-21 team, and in particular full-back Danny Rose, suffered abuse in Serbia on Tuesday while Lazio were fined £32,500 by UEFA for monkey chants by their fans during a Europa League tie against Tottenham.
Bernstein continued: "No player should suffer the intolerable abuse the likes of which Danny Rose was subjected to in Serbia."
- Sports & Recreation