Andrew Faulkner was a project engineer and team leader on the Square Kilometre Array, a ?1.3 billion project to build the world's most powerful radio telescope.
The tribunal heard that he had enjoyed a good working relationship with his line manager Peter Wilkinson, then UK head of SKA's design team, after joining Manchester's Jodrell Bank Centre for Astrophysics in 2004.
But relations had soured by 2007. Professor Wilkinson asserted that Dr Faulkner was taking too many decisions by himself, and he was also accused of not representing Manchester's interests vigorously enough. There was further acrimony when Dr Faulkner put forward a proposal on the future of the SKA project in November 2007 that would have sidelined research at Manchester in favour of work at the University of Cambridge, the tribunal heard.
Before a crucial funding meeting, Professor Wilkinson met Dr Faulkner to discuss the "communications fracture".
But the meeting on 4 December 2007 became an "unpleasant" confrontation, the tribunal judgment says, after the arrival of Mohamed Missous, professor of semiconductor material and devices at Manchester, and Lucio Piccirillo, professor of radio astronomy at the institution.
Professor Wilkinson confirmed to the tribunal that "feelings ran very high and some unnecessarily harsh remarks were made" during the three-hour meeting.
Professor Missous is said to have "conveyed his unhappiness" with Dr Faulkner's plans by "getting out of his chair and yelling at the claimant".
The tribunal was satisfied that Dr Faulkner had been "subjected to a barrage of shouting and verbal abuse" and "it was made clear to him he was a subordinate who had stepped out of line".
Dr Faulkner later submitted a complaint of "informal bullying" against his line manager, but this was rejected.
Despite apologies from Professor Wilkinson and Professor Missous, Dr Faulkner continued his complaint, but it was dismissed by an internal investigation.
The confrontation was deemed "a one-off incident at which harsh words had been spoken in the heat of the moment".
Dr Faulkner quit after being offered a senior research associate post at Cambridge in July 2008.
A tribunal has now ruled that Dr Faulkner was unfairly dismissed, stating that the ill-tempered row constituted a "fundamental and repudiatory breach of the contract of employment".
The judgment rejects the claim that the meeting was "an argument between mature and passionate people which was clumsily handled". It says it was "a completely unacceptable meeting, which wholly overstepped the boundary...of proper behaviour".
However, it rejects charges of bullying made against Professor Wilkinson and says that Manchester did not subject Dr Faulkner to any detriments through a breach of employment law.
The case follows a successful appeal by the university against an earlier tribunal ruling in 2009, which found in Dr Faulkner's favour.
A Manchester spokesman said: "The tribunal did not uphold the claim that Dr Faulkner was subjected to further detriments because he had made public interest disclosures. This key finding has been overturned as a result of the university's appeal."
A hearing to decide compensation is scheduled to take place on 14 February.
Keep watching the skies: tragic death will not delay 'most ambitious science project in history'
Dubbed "the most ambitious science project in the history of humanity", the Square Kilometre Array will be the largest and most sensitive radio telescope ever built.
It will be made up of 3,000 dishes, each about 15m wide, with a total collecting surface of about 1 sq km.
The dishes will be networked and spread over a continent - making it 50 times more powerful than any existing radio telescope array, with 100 times the resolution.
The location of the SKA is to be decided in March. The possibilities are either Australia and New Zealand or South Africa and other African states.
Run as an international partnership between 67 organisations in 20 countries, the scheme was conceived in 1990, when Peter Wilkinson wrote the first paper describing the basic concept.
The SKA was in the news earlier this month after the unexplained death of astrophysicist Steve Rawlings, a member of the project's founding board, who died at the Oxfordshire home of his colleague and friend of 30 years, mathematician Devinder Sivia.
Dr Sivia was arrested on suspicion of murder and held for 24 hours, but was released on bail.
Professor Rawlings' widow Linda released a statement saying that Dr Sivia should not be blamed for what she believed was a tragic accident.