Rejecting the argument that the schoolboy's death was an accident, Deputy Assistant Commissioner Bill Griffiths said: "The fact remains, as far as we're concerned, that this was the murder of a 10-year-old boy."
Detective Superintendent Trevor Shepherd, who led the investigation, said there was no evidence to bring a case against anyone else.
But he denied his team of detectives had failed, adding: "We did our job, I believe, as best as we could."
Extending the Met's sympathies to Damilola's family he said: "Not only have they had to endure his murder they've had to sit through a very difficult trial."
Unreliable
Speaking at a news conference after the two 16-year-old brothers were found not guilty Mr Griffiths rejected suggestions that the investigation was a "fiasco".
He said police had done their job and the fact the Crown decided to go to court proved there was a case for the brothers, and two boys acquitted earlier, to answer.
Commenting on the verdicts DS Shepherd said: "They are a disappointment to us. We accept the decision of the court and now we must move on from here."
But he added: "We used all resources available and no less effort was put into this inquiry than we would put into many major terrorist investigations."
He said a deep-rooted gang culture on the North Peckham estate, where Damilola died, meant few people were prepared to help solve his death.
'Difficult' witness
Mr Griffiths said police would take on board all the criticisms made by the judge, but said officers could not be held responsible for events in the courtroom.
He also stood by Sergeant Carolyn Crooks, the officer responsible for working with witness Bromley, who claimed she saw the attack which led to Damilola's death.
Although she was the key witness, Bromley's evidence was demolished in court and the judge ruled that it was too unreliable to be considered by a jury.
Mr Griffiths said Sgt Crooks had done a very professional job, working with a witness who had "difficulties".
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