Landscape charity The John Muir Trust sought a judicial review after SSE's 67-turbine Stronelairg project was given planning consent last year.
However, Lord Stones said minister's reached their decision "in breach of environmental obligations".
The judge ruled members of the public had been denied the opportunity to comment on a revised planning application for the project, while ministers did not take into account Scottish Natural Heritage's objection to any wind farm development at Stronelairg.
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He concluded: "The interest of any non-governmental organisation, such as the trust, is deemed sufficient. The question, therefore, is not whether the trust was prejudiced, but whether members of the public were prejudiced."
The Trust welcomed the decision, saying the area would have faced severe disruption as the result of excavating 22 million cubic feet of stone from the area.
Stuart Brooks, John Muir Trust Chief Executive, said: "This is great news for all those who love Scotland's wild land and wish to see it protected. A financial appeal brought a tremendous level of support from over a thousand well-wishers, allowing the Trust to proceed. Lord Jones has now decided the Trust's court action was well-founded."
A spokesperson for SSE said: "We are disappointed with the result of the judicial review of the consent decision for Stronelairg wind farm.
"We will now review the judgement in detail and consider our options accordingly."
(LM/JP)
