But they still continue to stand trial on a charge of indecent assault.
A third boy, also aged 10, was acquitted of indecently assaulting the girl.
A jury of eight men and four women returned not guilty verdicts on the direction of the judge, Mrs Justice Bracewell, following representations by defence lawyers on Monday.
Mrs Justice Bracewell said there was "a fundamental flaw" in the evidence in relation to the allegation of rape in that when the girl was interviewed and video recorded by the police woman she did not make any allegation of rape and the police woman asked a leading question which, in effect, put words into the girl's mouth.
The judge said the girl's answer was of "no evidential value, but it taints what comes thereafter."
In the circumstances it would "not be proper" for the jury to consider the count of rape against the two boys charged with that offence, she concluded.
The two boys are believed to have been Britain's youngest rape defendants.
A fourth boy, an 11-year-old cousin of the alleged victim, is also standing trial for alleged indecent assault.
They are alleged to have taken part in a sex attack on the girl, who is now aged 10, in the boys' lavatories at their school on May 6 last year.
All four denied the charges against them.
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