Professor Malory Nye had insisted he was forced out of his £67,000-a-year post at the Al Maktoum College because of his race and religion.
The institution offers post-graduate courses in Arab and Muslim studies and Mr Nye claimed senior figures wanted a Muslim in charge.
His wife Isobel Campbell-Nye, who was head of the English department, has also lost her unfair dismissal case.
The couple, who live in Perth, took the college to an employment tribunal earlier this year. They alleged there had been serious problems in the running of the institution.
However, employment judge Alan Strain ruled in the college's favour. A detailed written judgment will be released later, but the tribunal office in Dundee has confirmed all of the pair's claims have been rejected.
A spokesman for Al Maktoum College said: "The college welcomes the judgment of the employment tribunal.
"The ruling makes it clear that the college at no time engaged in any discriminatory activities or took any decisions based on grounds of race, sex or religion.
"The college continues to place diversity, religious pluralism and multiculturalism at the core of its higher education programmes as well as its day-to-day activities. We are now keen to move on."
During the tribunal, Mr Nye said the college had been "decapitated" and "left in chaos" after his departure.
He claimed there had been tensions in the administration team between people who were loyal to him and those loyal to Abubaker G Abubaker, the director of operations.
He said Mr Abubaker had tried to undermine him by writing letters of complaint to Lord Elder, the college's chancellor.
Mr Nye and his wife were suspended last June and dismissed just under a year ago.
In his evidence to the tribunal, Lord Elder denied any racial or religious motive for his actions.
He spoke of academic issues and internal staffing problems and said it had been "simply impossible" to consider Mr Nye continuing as principal.
He also said there had been issues of conduct and behaviour with Mrs Campbell-Nye and he believed she had gone beyond her job remit and was acting as her husband's chief of staff.
Al Maktoum College was founded in Dundee in the late 1990s with the support of Sheikh Hamdan Bin Rashid Al Maktoum, deputy ruler of Dubai.