Judge Eady QC dismissed all claims made by the vicar in the hearing at a court in London.
He had appealed against a decision made by Nottingham Employment Tribunal that he was not discriminated against.
In her ruling the judge agreed with the previous case that "the constitutional convention means that the State cannot impose same sex marriage upon the Church".
Canon Pemberton married Laurence Cunnington last April but had his right to officiate removed by the then acting Bishop of Southwell and Nottingham Richard Inwood following the wedding.
The clergyman then had a job offer as a chaplain for Sherwood Forest Hospitals Trust withdrawn, which he claims was caused by the Church of England discriminating against him because of his sexual orientation.
Bishop Richard told the tribunal same-sex marriage was against the church's beliefs.
In a statement Canon Pemberton thanked the judge "for the obvious care that she took to consider properly the novel and complex issues" raised.
He added: "The result is, obviously, not the one my husband and I had hoped for. I appreciate that this case was a source of hope for many people and I am grateful that the judge has recognised its significance and indicated that its importance warrants permission to appeal to the Court of Appeal.
"I am now going to take some time to consider the lengthy judgment with my husband, and we will decide on the best way forward, having taken advice from my lawyers."
In her judgement the judge accepted that in any other circumstances it would be "direct discrimination" but she stressed that the Church had an exception.
She ruled that the House of Bishops' Guidance, on entering into a same sex marriage was clear and that the priest would have known that getting married would have meant he would not be "of good standing".
Judge Eady QC concluded: "Given the importance of the legal questions involved and the novel issues arising... I would consider this matter suitable for permission to be given to appeal to the Court of Appeal, should such an application be made."
A spokesperson for the Diocese of Southwell and Nottingham said: "Churches across the diocese continue to offer a generous welcome to people from all backgrounds and we remain fully engaged in the Church's exploration of questions relating to human sexuality.
"The Church of England supports gay men and women who serve as clergy in its parishes, dioceses and institutions. It has no truck with homophobia and supports clergy who are in civil partnerships, as set out in the House of Bishops guidelines in 2006.
"We recognise that it has been a long and difficult process for all those concerned, and we hold them in our thoughts and prayers."
Speaking on Premier's News Hour, Rev Peter Ould, an Anglican priest who comments on sexuality issues says the Pemberton case is significant.
He said: "The original employment tribunal ruling was very clear and all employment appeal tribunal has done is to uphold that ruling but, interestingly, it does so at a point in the judicial system where it now becomes a precedent in law.
"Any similar priest could be turned down and the bishop would essentially say 'Well, look at the Pemberton ruling - I'm just doing the same thing.'"
Click here to hear Rev Peter Ould speaking with Premier's Antony Bushfield: