An independent panel found the Chelsea skipper guilty of racially abusing the QPR defender, and he has since decided not to appeal the four-match ban and fine imposed on himJohn Terry, claiming that "the reputation of English football has been damaged" by recent events involving the Chelsea captain.
Terry announced earlier this week that he would not be appealing the governing body's decision to ban him for four matches and fine him £220,000, after he was found guilty by an independent panel of racially abusing Anton Ferdinand.
And in a statement by the FA, Bernstein condemned the defender's actions, and called for lessons to be learned in the aftermath of the affair.
"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," he 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."
Bernstein also highlighted the abuse suffered by Danny Rose and other England Under-21 players in Serbia on Tuesday as evidence that the battle against Racism was a widespread one.
He added: "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.
"No player should suffer the intolerable abuse the likes of which Danny Rose was subjected to in Serbia.
"Domestically The FA has ultimate responsibility for the leadership of the game at every level and I, personally, remain determined to lead English football in this fight.
"This coming fortnight’s ‘Kick It Out’ campaign is a valuable reminder of the strength of the game when addressing these issues together, and it is this positivity that our game must harness."