He said the Brazilian electrician's death was a tragedy, and offered his condolences to the dead man's family.
Speaking at the Oval cricket ground in south London after the verdict on Friday, Mr Stephenson said: "The death of Jean Charles de Menezes was a tragedy. He was an innocent man and we must and do accept full responsibility for his death."
"For somebody to lose his life in such circumstances is something the Metropolitan Police Service deeply regrets.
"I wish once again to extend my profound condolences to the family of Jean Charles. They have suffered the most dreadful of losses."
He said the suicide bombings of July 7 and the failed suicide attacks on July 21 had created a unique situation in the capital, with terrorists on the loose.
"No-one set out that day to kill an innocent man," he said. "The coroner has ruled that, on the extensive evidence put to the court, this was not an unlawful killing."
He said the officers who shot the Brazilian "set out with the intent to protect and defend the public,
A jury rejected the police account of the shooting of Jean Charles de Menezes as the Brazilian's inquest was branded a "whitewash" by his family. After returning an open verdict, the 10 jurors rejected a string of claims made by officers about the events leading up to Menezes being killed.
In a damning indictment, they dismissed claims by firearms officer C12 that he shouted "armed police" before opening fire. The jury also disputed that the 27-year-old Brazilian had walked towards officers before he was killed.
The jurors concluded that six police failings caused or contributed to the innocent man's death.
Firearms officers shot Menezes at Stockwell Tube station in south London on July 22, 2005, after mistaking him for failed suicide bomber Hussain Osman.
As the jury returned its verdict after its sixth day of deliberations, the Menezes family accused coroner Sir Michael Wright of "presiding over a complete whitewash."
In a stinging attack on the coroner, they said he "failed on every count" during proceedings.
A family statement, released through the Justice4Jean campaign group, said: "After three months of evidence, 100 witnesses and millions of pounds, the coroner, Sir Michael Wright, has presided over a complete whitewash. He has failed on every count of the purpose of an inquest investigation."
Following the verdict at the inquest into the death of Jean Charles de Menezes Acting Commissioner Sir Paul Stephenson said:
"Over the past ten weeks the inquest has heard in great detail about the events of 22nd July 2005 and what unfolded on that tragic day over a very short space of time.
"We have heard the jury's conclusions and now need to take time to give proper consideration to them. I also note the coroner's intention to make a report on his recommendations for any future action we may need to take.
"The death of Jean Charles de Menezes was a tragedy. He was an innocent man and we must, and do, accept full responsibility for his death.
"For somebody to lose their life in such circumstances is something that the Metropolitan Police Service deeply regrets. In the face of enormous challenges faced by officers on that day we made a most terrible mistake.
"I am sorry.
"I wish to once again express my profound condolences to the family of Jean Charles. They have suffered the most dreadful of losses.
"July 2005 brought with it unparalleled challenges for the Met and the people of London including the unique situation where there were four failed suicide bombers on the run.
"Our priority that day was to arrest these terrorists before they could commit further atrocities and potential acts of mass murder.
"No-one set out that day to kill an innocent man.
"The Coroner has ruled that on the extensive evidence called before him this was not an unlawful killing.
"Those officers knew that further terrorist attacks could take place. They set out with the intention to defend and protect the public.
"The officers involved in the fatal shooting of Jean Charles have described in court the personal impact this tragedy has had and will continue to have on their lives for many years to come.
"Our duty then, as it is now, is to ensure that this organization learns from the events to minimize the chances of this ever happening again.
"Since July 2005 the Met has been the subject of numerous reviews and inspections. These have ensured we have identified the areas where we believe things needed to be changed.
"As the leader of this organization, it is my duty to ensure that the appropriate lessons are learnt and acted upon. That is what we have done and will continue to do.
"The extraordinary events of July 2005 will be remembered by Londoners and indeed across the world. It was a time when 52 people had lost their lives, 977 were injured and many others were living in fear of further terrorist attacks – a threat that continues to this day.
"Therefore, our priority is to protect Londoners by stopping those who are intent on terrifying us all. In doing that we must learn from the terrible tragedy of Jean Charles' death. Thank you."
Mercopress