Videos circulated on the internet in the aftermath of Sunday's game, with some claiming the footage shows Terry insulting Ferdinand using racist language.
Terry has denied racially abusing Ferdinand, who he admitted had accused him of making a racist remark, but insisted his own response was actually a denial and not racist in any way.
Ferdinand met with QPR representatives and manager Neil Warnock at the Hoops' Harlington training ground to discuss the issue and decided to complain to the FA - a move which could have huge implications for Terry's future in the game.
An FA statement read: "The FA can confirm it has received a complaint relating to an alleged incident of racist abuse in the QPR versus Chelsea fixture at Loftus Road on 23 October 2011.
"The FA will now begin to make enquiries into this matter.
"The FA takes seriously any allegations of discrimination and abuse of this type."
Terry met with Ferdinand in the away dressing room at Loftus Road following the R's 1-0 win in an attempt to persuade the 26-year-old that he did not racially abuse him.
The England captain then released a statement saying he was "disappointed" that some people had come to the "wrong conclusions" about the supposed context in which he had made the comments towards Ferdinand, adding: "I thought Anton was accusing me of using a racist slur against him. I responded aggressively, saying that I never used that term.
"I would never say such a thing, and I'm saddened that people would think so."
The investigation marks another chapter in what has been a turbulent 12 months for the Chelsea defender.
Terry was stripped of the England captaincy in February 2010 amid allegations that he cheated on his wife with the ex-girlfriend of former team-mate Wayne Bridge.
Terry received widespread criticism after rumours of the alleged affair surfaced, but England boss Fabio Capello reinstated the Blues defender as national skipper in March.
Chelsea manager Andre Villas-Boas offered his full backing to Terry this afternoon over the alleged comments he made towards Ferdinand.
Villas-Boas said: "He's put out his statement and we fully back John. John is a player who represents this country to the highest level internationally.
"He is a player of great responsibilities for the country and he is confident about it because he spoke to Anton after the game.
"For us it was end of story and it still is. It's just a great misunderstanding and something blown out of proportion.
"John Terry represents this country internationally and it should also be that people who represent this country should have better and fuller support instead of stories based on speculation."
Villas-Boas' comments came hours after police confirmed that they are "assessing" claims Terry racially abused Ferdinand after receiving a complaint from a member of the public.
Terry said that he would fight to clear his name and welcomed the news in a statement which read: "I welcome the FA enquiry and look forward to clearing my name as soon as possible.
"Until then I have no further comment."
Terry and Ferdinand have known each other for over 10 years as the former played for the same boys' team as Ferdinand's cousin, Rio, as a youth.
The QPR defender is yet to speak publicly on the matter, but he has been offered the full backing of his club over the alleged incident.
Chairman Tony Fernandes said: "Queens Park Rangers Football Club does not condone racism in any way, shape or form.
"As a club, we will provide our players with our unequivocal support when alleged incidents like this occur.
"The club has, and will continue to support Kick It Out's One Game, One Community initiative, football's equality and inclusion campaign.
"However, we are keen to draw a line under this alleged incident and focus on our forthcoming fixtures, starting with Sunday's London derby at Spurs."
Chelsea reiterated their support for Terry following the announcement.
"John has issued a statement categorically denying any allegations of racist abuse. We stand by John and his statement," a Chelsea spokesman said.
"Chelsea Football Club finds all forms of discrimination abhorrent and we are proud of the work our players and staff undertake campaigning on this important issue.
"We look forward to the conclusion of the FA's investigation and won't be commenting further on the matter until that time."
Anti-racism group Kick it Out admitted that it was disappointed to hear of the charge, especially given that it comes so soon after Patrice Evra accused Luis Suarez of racism on the pitch during Manchester United's game at Liverpool 10 days ago.
Kick it Out chairman Lord Herman Ouseley said: "It is of great regret that in Kick It Out's One Game, One Community weeks of action, backed by all 92 professional clubs, two high profile incidents of alleged racist abuse have taken place.
"This is worrying and potentially very damaging; what happens at the top end of the game has an impact at grass roots level and at parks pitches across the country.
"Kick It Out condemns discrimination in any form and hopes matters are investigated properly.
"In the meantime, the work Kick It Out does with groups and individuals, including players and fans at professional and community level, will continue in stamping out discrimination and unacceptable behaviour in all its forms."