Embarrassed bosses acted swiftly on the back of revelations that Sam Kay, of Corpus Christi College, Oxford, had actually graduated in June 2008 and was working as an accountant.
The Manchester University team, beaten in the final by 275 points to 190, were named the winners of the 2009 contest after a BBC investigation, conducted with programme makers Granada, ruled that Corpus Christi had broken the rules.
A joint statement said: "The University Challenge rules on student eligibility are that students taking part must be registered at their university or college for the duration of the recording of the series.
"Whilst obviously not intending to, Corpus Christi broke this important rule, where other universities and colleges taking part adhered to it.
"We therefore find ourselves in the regrettable position of having no choice but to disqualify Corpus Christi from the final. This means they forfeit their hard-fought title, which now goes to the Manchester University team."
Mr Kay, who was still a student when the first two rounds were filmed and went on to graduate with a first in chemistry, had earlier said he believed he had done nothing wrong.
The final, hosted by Jeremy Paxman, was filmed two months ago and screened on BBC2 last month.
It attracted five million viewers – up two million on the climax of last year's contest. Much of the attention was on the Corpus Christi captain, Gail Trimble.
She had been dubbed "the Human Google", after scoring two-thirds of her team's 1,200 points on their way to the final.
But their triumph was overshadowed by weekend claims they had broken the rules.
By the time the final was filmed, Mr Kay was working full-time as a graduate trainee for the accountancy firm PricewaterhouseCoopers.
He said yesterday: "I hugely regret not confirming my change of status to the University Challenge programme-makers before the final rounds.
"I had honestly believed I was eligible, as I had indicated my course dates when I applied. I can only apologise to the other competitors and especially to my team, as it was never my intention to mislead anyone."
Matthew Yeo, captain of the Manchester University team, had earlier said they had no desire for a rematch and insisted Corpus Christi were "worthy champions".
In a statement, Corpus Christi College said its students had entered the programme in "good faith".
The BBC was at the centre of a storm of controversy earlier this year after presenter Carol Thatcher was dropped from The One Show for referring to a leading tennis player as a "golliwog" in front of guests in the programme's green room.
Days later, the corporation decided an apology from presenter Jeremy Clarkson was sufficient after he branded Gordon Brown, the Prime Minister, a "one-eyed Scottish idiot".
Jonathan Ross has only recently returned to work after being suspended for three months after he and Russell Brand left obscene messages on the home answering machine of the actor Andrew Sachs.
The corporation also came under fire from fans of Strictly Come Dancing last year over the handling of the most recent series, which was dogged by voting problems and claims that the result was "a fix".