Chelsea skipper Terry decided not to appeal against a four-game ban for using racist language towards Queens Park Rangers defender Anton Ferdinand on Thursday, bringing to a close an unsavoury chapter that put racism under the microscope.
Terry, who was cleared in a lawcourt of racism in July, apologised for his "inappropriate" language on Thursday although he continued to express "disappointment" at the FA's ruling.
Bernstein said having football dragged through the lawcourts marked a difficult period for the English game which has made large strides in erasing racism from stadiums.
"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 in a statement.
"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 learned 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."
The FA have complained to world governing body FIFA after Tuesday's under-21 match in Serbia was marred by incidents of alleged racist abuse towards England's black players.
While campaigns in England such as "Kick it Out" have been successful in the fight against discrimination, the Terry affair which has rumbled on for a year and led to the resignation of former England coach Fabio Capello as well as his own retirement from international football, have cast a cloud over the game.
"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. However, we too will learn from the case," Bernstein said.
Bernstein rejected criticism over the length of time it took to punish Terry for the incident in Chelsea's Premier League game at QPR last October.
"I understand the concern about the time the process took but the most important thing was getting it right for all the concerned parties," he said.
"I can appreciate that many observers believed The FA's investigation was overly delayed and, ideally, we would have operated on a short time frame, not least due to the impact this process has on individuals and their families and the resultant stress and loss of trust.
"Had there been no criminal investigation and prosecution, it is likely that this case would have been concluded in a matter of weeks."
Terry, who was also fined 220,000 pounds by the FA, also faces disciplinary action by Chelsea although he has not been stripped of the club captaincy.
He begins his four-match ban in the away fixture at Tottenham Hotspur on Saturday.
