Premier can reveal Nottingham Employment Tribunal has dismissed all claims made by the vicar.
It ruled that "the constitutional convention means that the State cannot impose same sex marriage upon the Church".
Canon Pemberton has told Premier his lawyers were preparing grounds for appeal.
He 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The clergyman then had a job offer as a chaplain for Sherwood Forest Hospitals Trust withdrawn, which he claims was caused by the Church of England discriminating against him because of his sexual orientation.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.
Speaking on Premier's News Hour in August 2014 Canon Pemberton said: "I've never had any disciplinary process, this has entirely been done at the whim of one bishop.
"In another diocese I've received a rebuke and retain a full license.
"So I'm licensable in Lincolnshire but not so in Nottinghamshire - I don't think that's fair treatment."
A spokesperson for the Diocese of Southwell & Nottingham said: "We are thankful to the tribunal for its work on this complex case and for its findings in favour of the former Acting Diocesan Bishop, the Rt Revd Richard Inwood, on all the claims made against him.
"We recognise that it has been a long and difficult process for all concerned, and we continue to hold them in our thoughts and prayers.
"Churches across the diocese continue to offer a generous welcome to people from all backgrounds. We remain engaged in the on-going shared conversations across the wider Church of England that are exploring questions relating to human sexuality."
In their ruling the tribunal panel said the case had "profound implications" for the Church of England.
It said that Canon Pemberton had been warned of the consequences by the Church if he went ahead and entered a gay marriage.
Bishop of Sherwood Rt Revd Anthony Porter wrote to him saying it would not be "appropriate conduct".
Canon Pemberton replied to the bishop saying the Church's teaching was "of doubtful legality".
"It is a core part of the qualifying of a priest for ministry within the Church that he confirms to Canonical Obedience," the ruling said.
It went on: "It matters not what we think about the appropriateness of the doctrine to current times. It is not for us to reconstruct the Church's doctrines.
"Furthermore the transition between civil partnerships and same sex marriage, summarised by the Bishop of Buckingham as 'civil partnership max' is irrelevant.
"We reiterate: there is the distinction between the Church and State,
"The constitutional convention means that the State cannot impose same sex marriage upon the Church".
Revd Peter Ould, a Church of England priest who speaks on issues of sexuality, told Premier it was a "fantastic ruling for the Church".
"The employment tribunal is very clear that the Church of England has the right to sign its own doctrine of marriage and to ask its clergy to abide by it".
He added that the ruling showed "there is no legal danger to the Church of England to continue to say that marriage is only between a man and a woman and that its clergy need to abide by that doctrinal view".
Revd Peter Ould speaking to Premier's Antony Bushfield: