Mr Justice Lindblom, ordered Pickles to reconsider the controversial proposal, which would involve more than 90,000 solar panels.
Planning permission has already been granted for a smaller solar farm at the site, but the company now hopes it will be able to secure planning permission for the larger development on the 46-hectare site – equivalent to almost 65 football pitches - adjacent to Ellough Airfield on Benacre Road, Beccles.
Developer Lark Energy claimed that the communities secretary had wrongly rejected its application, despite his own planning inspector finding that the solar farm would cause only limited harm to its surroundings and would not have significant environmental effects.
The inspector had found that the proposal complied with development plan policies and recommended granting permission.
And, upholding the claim, the judge said: "The decision letter contains an assessment of the planning merits which is clearly at odds with the inspector’s."
He found that the communities secretary’s reasons left "genuine doubt" that he had made his decision properly in accordance with the 2004 Planning Act.
The judge rejected three other grounds of challenge, but quashed the decision and ordered the matter to be reconsidered in the light of his ruling.
The scheme was originally rejected by Waveney District Council, against the recommendation of its own planning officer, in February 2013.
The secretary of state rejected Lark Energy’s appeal in October 2013.
In between, in April 2013, the council granted permission for a much smaller solar farm on about 29 hectares in the northern part of the site.
Lark Energy Limited v Secretary of State for Communities and Local Government. Case Number: CO/17111/2013
Read Planning's latest report on solar development here