Mr Bloomberg has spoken negatively of the initiative for the first time, ahead of a potential bid for the presidency.
The policing strategy was disproportionately used against ethnic minorities in the city during his three-term tenure as mayor.
Now Mr Bloomberg has said he considers it to be a blight on his record – despite defending its use earlier this year as having brought down the crime rate in the city.
Addressing a black church in Brooklyn, Mr Bloomberg said he was "sorry", adding "I can't change history… however today, I want you to know that I realise back then I was wrong."
However he is understood to have registered to appear on ballots in at least one state ahead of the Democratic convention where the nominee is ultimately named – vying for the attention of voters in the Alabama presidential primary.
Now - much like Joe Biden’s pre-race apology for imposing stiffer sentences on crack cocaine users, and Hillary Clinton’s apology for branding black American youths “super predators” before her 2016 nomination - Mr Bloomberg appears to be distancing himself from a past political manoeuvre accused of harming black communities.
Attempting to put the decision to expand the policing policy into context, he noted there were around 650 murders a day in the city when he took office in 2001. He said “I was not going to accept that — and I didn't.
“I was determined to improve police-community relations while at the same time reducing crime even further."
However, he added: “The fact is, far too many innocent people were being stopped while we tried to do that.
“The overwhelming majority of them were black and Latino.
"That may have included, I'm sorry to say, some of you here today. Perhaps yourself or your children, or your grandchildren, or your neighbours, or your relatives."
It is unclear how far his apology will go in easing anger from communities affected by the policy.
One activist, DeRay Mckesson, said "It is convenient that Bloomberg suddenly apologises but has done nothing to undo the immense damage he has caused on countless lives.
"His apology is not accepted."
Stop and frisk targeted black men with startling regularity. At the policy’s peak under Mr Bloomberg in the first three months of 2012, some 203,500 people were frisked by police.
Black people made up more than half of the subjects of stop and frisk incidents over that period – 108,097 searches in total – despite the city’s black community making up roughly a quarter of its overall population at the time.
The number of white people stopped and searched over the same period was 18,387.
"Under Bloomberg, NYPD increased stop and frisk from 100,000 stops to nearly 700,000 stops per year. Ninety per cent of those impacted were people of colour — overwhelmingly black and brown men," black activist and data scientist Samuel Sinyangwe tweeted on Sunday.
"Bloomberg personally has the money to begin paying reparations for this harm. 'Sorry' isn't enough."
Renowned civil rights activist Reverend Al Sharpton however applauded Bloomberg for reversing his stance - though he added that he would have to "wait and see whether it was politically motivated."
"As one who helped lead countless demonstrations, marches and rallies to amplify the racial impact that was had on the Black and Brown community from stop-and-frisk policing, I am glad to see Mr Bloomberg now admit that the policy was wrong," Rev Sharpton said.
"It will take more than one speech for people to forgive and forget a policy that so negatively impacted entire communities."
Additional reporting by AP.