The employment tribunal said John Reaney, 42, was discriminated against "on grounds of sexual orientation" by the Hereford diocesan board of finance.
Mr Reaney, from Colwyn Bay, Conwy, said he was "delighted" at the decision.
The Bishop of Hereford, the Rt Rev Anthony Priddis, said he was "naturally disappointed" and may appeal.
Delivering the judgement, the tribunal said the case would now be listed for a remedy hearing.
"The respondents discriminated against the claimant on the grounds of sexual orientation," said the judgement.
Mr Reaney, who had already worked in two other Anglican dioceses, where he had been praised for his achievements, said he was delighted.
He said the case "demonstrated to many lesbian and gay Christians working for God within the Church of England that they are entitled to fair and respectful treatment".
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