William Kadama had been on life support at Great Ormond Street Hospital in London since being pulled from the pool unconscious on 30 July.
His best friend Gameli Akuklu, also 14, was pronounced dead at Northwick Park Hospital on the day of the tragedy.
A post-mortem examination later confirmed the cause of death as drowning.
'Extremely distressing'
Metropolitan Police Assistant Commissioner Bernard Hogan-Howe said: "I wish to express my deepest sympathy and condolences to the family and friends of William Kadama following his tragic death at Great Ormond Street Hospital this morning.
"This is an extremely distressing time for all concerned and we will continue to provide family liaison officer support to both William's and Gameli's families."
He added: "The death of Gameli Akuklu was extremely distressing, and the death of William is equally tragic.
"Our sympathy is with the family and friends of both the boys at this time."
The incident happened when the teenagers were taking part in a council-run scheme to keep youngsters busy during the summer holidays.
Both boys were discovered underwater and unconscious and a lifeguard pulled them out.
Remained unconscious
William's parents, who were originally from Uganda, are both dead but his aunt Mary, an IT lecturer at Barnet College, prayed for him at a special church service last Sunday.
More than 300 people joined families of both the youngsters at the International Gospel Church in Burnt Oak, north London, to pray for William and pay their respects to Gameli.
William, who was from the Barnet area, never regained consciousness after the tragedy, police said.
A Met spokesman said the decision to switch off the life support machine was a joint one between William's family and doctors.
A post-mortem examination is expected to be carried out on Wednesday and an inquest will be held in due course, the spokesman said.
An investigation into the tragedy is under way, supervised by the independent Police Complaints Authority.
The Health and Safety Executive has also been notified and will conduct its own investigation.