Hartmut Zapp had argued that he was leaving "the public body of the Church" but not the community of the faithful.
But the court determined that a person cannot partially leave the Church, and referred to the bishops' new decree on church tax.
As far as the state was concerned, Zapp had left the Church, Judge Werner Neumann said.
Catholics in Germany have to pay an extra 8-9 per cent of their annual income tax to the Church.
The German bishops' conference published a decree last week stipulating that priests must tell parishioners who opt out of paying the tax that they will be excommunicated as a result.