The two boys sustained serious head injuries while a third boy, also nine, suffered leg injuries and was also taken to hospital.
The boys were waiting to have a turn in nets at the Spencer Cricket Club in south London when the tree came down at around 3.45pm.
It is believed that adults then lifted the fallen tree enough to get the children out from underneath.
Charlie Masson-Smith, of Wandsworth Council, said yesterday’s “very strong” winds could have knocked down a healthy tree at the private cricket ground.
He said: “It is a terrible accident. From what we have been told there were a bunch of kids queuing up to go in the nets. All of a sudden this tree came down on them.”
A Metropolitan Police spokesman said: “We were alerted by the ambulance service that a tree had fallen on children at Spencer Cricket ground.
“Three boys were taken to St George’s Hospital in Tooting. Two had head injuries and were in a serious condition. The third had leg injuries and was described as walking wounded.”
Spencer Cricket ground is home to the private Spencer Club, a sports club with more than 500 members offering cricket, tennis, squash, hockey and lacrosse.