Paramedics arrived to "a scene of carnage" with "distressed and overwhelmed children and teachers".
A sports utility vehicle smashed through the wooden wall of the school in Sydney's west, where 24 primary-age children were in class with their teacher, police said in a statement.
Police confirmed the boys, both aged eight, suffered cardiac arrest and died in hospital.
One of the first responders, a local resident, helped lift the two-tonne SUV, which had trapped one of the boys who later died. 'There were a number of distressed and overwhelmed children and teachers at the scene of a awful accident'.
She was reportedly dropping off a child at the time.
Acting Assistant Police Commissioner Stuart Smith said: 'We're not looking this as an intentional act'.
Two eight-year-old boys have died and another three girls are in hospital, after a Toyota crashed into a classroom in the Sydney suburb of Greenacre.
"He was saying "I want my mum".
"Obviously they were crying, they were distressed, some were asking for their parents, that's a natural response in such a bad set of circumstances".
Two chaplains were brought in to the school to support the victims.
Maha Al Shennag, 52, who was behind the wheel of the Toyota Kluger, has been charged with two counts of risky driving occasioning death and one count of negligent driving occasioning death.
Channel 10 reporter Andrew Denney tweeted from scene that police will allege the driver was "distracted by something in her car" before losing control.
The woman, who screamed "help, I'm sorry" after the crash has been charged with two counts of unsafe driving occasioning death and suspended her licence.
Her licence was suspended and she was granted conditional bail ahead of an appearance at Bankstown Local Court on November 29.
Police are asking parents who wish to collect their children to attend the Boronia Road school entrance.
It is understood that at least three other children sustained minor injuries, such as broken bones and cuts.