Birmingham City Council had refused consent and their decision was backed by a government inspector on an appeal by the church.
Now though the judge has formally quashed the decision of the planning inspector, after being told that the country's planning supremo, communities secretary Hazel Blears, has conceded that the decision should not stand.
At a brief hearing Mr Justice Newman ordered Blears to have the matter reconsidered.
The Secretary of State had also agreed to pay the Oratory Fathers' reasonable legal costs of challenging the council's decision.
The judge was told that, having considered the decision, Ms Blears conceded that her inspector's finding was erroneous in law.
She considered he had failed to give adequate reasons on his consideration of the relative impact of the palisade fencing when compared with the type of fence that would be permitted under General Permitted Development rules, without the need for any planning permission.
The Birmingham Oratory is a Catholic oratory and church, also known as Little Rome, at which Lord of the Rings author JRR Tolkien worshipped for seven years.
It is based at The Oratory, 141 Hagley Road, Edgbaston.