Rt Revd Alan Wilson said the church teaching that "marriage is...of one man with one woman" is "not much of a definition".
He made the comments speaking at the employment tribunal of Canon Jeremy Pemberton, who married his same-sex partner last year in a civil ceremony.
Mr Pemberton was one of the first clergy members to marry his same-sex partner and as a result has brought a case against Rt Revd Richard Inwood, the former acting bishop for the Diocese of Southwell and Nottingham.
He claims that his job as a hospital chaplain in Nottinghamshire was revoked after his ceremony with his partner, as was his permission to officiate in June 2014, which he said breached the Equalities Act.
The Church's case claims marriage consists of the partnership between a man and a woman and is enshrined in Church doctrine.
However Mr Pemberton's lawyers say that the bishop broke the law when he revoked Mr Pemberton's job.
The Bishop of Buckingham, appearing for Mr Pemberton, was asked by Thomas Linden QC, for the respondent Bishop Inwood, if he thought clergy "should accept the teachings of the Church". He replied: "Yes."
Asked about the Church's teaching on "holy matrimony", he said: "It's not that I don't think it's true, or the canons of England should not be followed, all I say is it's a lousy definition, if it cannot tell you who is and who is not married."
He added the definition of heterosexual marriage was "entirely coincidental because of the time it was framed".
The tribunal panel also heard that Mr Pemberton had not been told or consulted about a Church of England press statement being drafted to explain his marriage to Laurence Cunnington in April last year.
It was reported that a series of drafts went through the Archbishop of York's office but had never been shown to him.
The Church of England has defended its treatment of Mr Pemberton. A spokesperson said: "The Church supports gay men and women who serve as clergy in its parishes, dioceses and institutions.
"Jeremy Pemberton is one of many who currently serve and receive that support.
"The Church has no truck with homophobia and supports clergy who are in civil partnerships."
But it also added that the Church of England's doctrine on marriage is clear.
"The Church quite reasonably expects its clergy to honour their commitment to model and live up to the teachings of the Church.
"Clergy do not have the option of treating the teachings of the Church as an a la carte menu and only modelling those with which they personally agree.
"The Church is currently involved in a process of shared conversations about a range of issues on sexuality, in regions across the country.
"It is regrettable that this case risks undermining that process by invoking legislation which does not even apply to this situation."