The ruling was made during the summer at the Upper Tribunal in London in the case of a 13-year-old boy who was excluded from school due to behaviour linked to his autism.
Under the Equality Act children with autism and similar conditions are not treated as disabled in relation to their behaviour. In addition, schools are not required to justify that a decision to exclude disabled children due to their behaviour is proportionate.
However, Judge Rowley said that this was in breach of the child's and other children's human rights and ruled that their behaviour in schools "is a manifestation of the very condition which calls for special educational provision to be made for them".
He added: "In that context, to my mind it is repugnant to define as 'criminal or antisocial' the effect of the behaviour of children whose condition (through no fault of their own) manifests itself in particular ways so as to justify treating them differently from children whose condition has other manifestations."
Jane Harris, director of external affairs at the National Autistic Society, which provided evidence in the case, described the ruling as "a landmark verdict".
"It could transform the prospects for future generations of children on the autism spectrum, by helping them get the education they deserve," she said.
"The government should recognise this decision and act immediately to make sure that autistic children are no longer unfairly excluded from school.
"Being autistic means someone sees, hears and feels the world in a different, often more intense way than other people, which can make school an overwhelming place.
"Without the right support, things like having a quiet place to retreat to when it gets too much or adapting communication strategies to their needs, autistic children can become highly anxious.
"In some cases, children can become so overwhelmed that they can't control their behaviour, which others can misinterpret as them being naughty or disruptive, when in fact they're extremely distressed.
"Exclusions should only happen as a last resort, when schools have tried every other practical solution."
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Melanie Field, executive director at the Equality and Human Rights Commission, which helped fund the 13-year-old boy's case, said: "We funded this case as we were concerned that children whose disability can result in them being more likely to be aggressive were being unfairly denied access to education.
"We are delighted with this judgment which will require schools to make reasonable adjustments to try to prevent or manage challenging behaviour and justify that any exclusion in these circumstances is proportionate.
"This is a positive step towards ensuring that everyone has the opportunity to reach their potential through education and increasing the inclusion of disabled children in mainstream education."
Polly Sweeney, human rights partner at Irwin Mitchell, which represented the boy's family, stressed that the ruling does not mean that schools are prevented from excluding children if it is necessary and proportional.
"However, it will ensure all disabled children are afforded the same safeguards, protections and rights under the law regardless of whether their disability gives rise to challenging behaviour," she said.
Matthew Dodd, head of policy and public affairs at the National Children's Bureau, said: "This judgment represents a long awaited victory for common sense and should help protect disabled children from being excluded from school unjustly. Depriving a disabled child of a mainstream education on the basis that they have a ‘tendency to physical abuse' without putting in place the right support to meet their needs, is a questionable defence for schools at best.
"The judgment rightly prevents schools from making this argument and we urge the government to change the law so that disabled children are not caught up in regulations that were clearly meant to prevent adults with criminal tendencies from protection under the Equality Act."
Pupils with SEND accounted for 46.7 per cent of all permanent exclusions and 44.9 per cent of all fixed exclusions in 2016/17.
Ex-children's minister Edward Timpson is conducting a review of school exclusions, looking at issues such as the high proportion of SEND pupils affected.
"The government is fully committed to protecting the rights of children with disabilities, as well as making sure schools are safe environments for all pupils," said a Department for Education spokesperson.
"We will be carefully considering the judgment and its implications before deciding the next steps."