The judge, Mr Justice Holman, ruled that education secretary Michael Gove had acted unlawfully by failing to consult on the move.
The £55bn BSF scheme was axed last year, leaving many councils with millions of pounds wasted on project development costs. The councils of Waltham Forest, Luton, Nottingham, Sandwell, Kent and Newham combined to mount a legal challenge.
In five of the cases the failure was "so unfair as to amount to an abuse of power", said the judge. He said that the government must now reconsider its decision.
The judge said: "However pressing the economic problems, there was no overriding public interest which precluded consultation or justifies the lack of any consultation."
A Department for Education spokesman said that in fact the judge did not call into question the decision to end the Building Schools for the Future programme, adding:. “On the substantive points he concluded that it was a rational decision and that the authorities involved had no expectation of being allowed to proceed with their projects."
Chris Keates, general secretary of teachers’ union NASUWT said: "The councils involved are to be congratulated for making a stand on this issue. The coalition government has shown time and again a reckless disregard for due process and consultation.
"Teachers, pupils, parents, and local councils were all sidelined. Since 12 May, programmes, grants and organisations have been thoughtlessly abolished with little, if any, regard for the consequences.
"BSF was a classic example of this, and it's now come back to bite the Secretary of State."
The secretary of state scrapped 715 school schemes in June when he announced that all BSF projects that had not reached financial close would not go ahead. Many councils had already spent millions on the projects. Kent County Council, for example, had spent £3.7m on consultants for cancelled schemes in Thanet and Gravesham, £2.9m on 16 schemes in Dover and Shepway, and £150,000 on proposals for schools in Sittingbourne.
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