In a ground-breaking move, Mr Justice Dyson upheld an application by Warwickshire County Council for a judicial review of her decisions and ordered that the authority's costs be paid.
He stopped short of ordering a new ballot but told Mrs Shephard to reconsider her decision.
The Government was "considering its position" as The TES went to press, and a spokesman for the Department for Education and Employment said: "A decision about whether to appeal will be made shortly."
John Airey, chair of Warwickshire's education committee, was delighted with the court's ruling. "This is wonderful news," he said.
Warwickshire sought a judicial review after Mrs Shephard admitted that parents of pupils at Stockingford Infant and Junior schools had been given misleading information during campaigns for grant-maintained status but failed to order a fresh ballots.
In the past month she has made similar decisions over opt-out ballots at two other schools, one in the Prime Minister's constituency and another in Nottinghamshire.
The High Court ruled this week that her decision over the Stockingford schools was "irrational" and therefore could not stand.
Mr Justice Dyson agreed that parents could have been misled by letters claiming that seven or eight jobs would go unless the schools opted out, when only one teaching job was later lost.
The schools, in Nuneaton, voted for grant-maintained status more than a year ago and had originally planned to opt out in April.
The latest Department for Education and Employment information on grant-maintained schools indicated that Mrs Shephard was "minded to approve" their applications. The matter is now in her hands.
Mr Airey described the High Court ruling as a victory for common sense and fairness. "It is an earth-shattering judgment and shows the legislation on grant-maintained ballots is in a mess," he said. "We launched this challenge because we were very concerned that misleading information had been given to parents who were asked to vote on the future status of these schools. The verdict was vital because such important issues were at stake."
Eric Wood, the county education officer, said: "The rights of parents to have clear and honest information is paramount, and due process must be followed if they are to make an informed decision."