He blames the situation on staff being absent on sabbatical leave and alleges that medical information about him was not submitted to the examiners by a tutor.
But Oxford say Mr Siddiqui's claim that he had lost out in his career was "complete speculation and fanciful".
Mr Siddiqui, 39, who has put his claim at £1 million, says he would have become an international commercial lawyer if he had gained the top qualification at the end of his time at Brasenose College.
He claims that his clinical depression and insomnia have been significantly exacerbated by his "inexplicable failure".
At the High Court in London on Tuesday, his counsel Roger Mallalieu told Mr Justice Foskett that in 2000, Mr Siddiqui was a "driven young man" aiming at a postgraduate qualification at an Ivy League university before a career at the tax bar in England or a major US law firm.