Governors decided remove Dr Patrick Lavery after fury at plans to sack 50 in a reorganisation axing half management posts.
The move is the latest in a catalogue of troubles at the college. Around 30 lecturers recently took voluntary redundancy at the college which is struggling with Pounds 1.2 million debts. The four-yearly Further Education Funding Council inspection is due next week.
The "coup" led to accusations form the Association of Principals of Colleges that over-zealous governors with insufficient training and experience are hounding heads out.
Bernard Smith, APC president, said his members operated under huge financial and personal pressure. "Often the principal is a target for misrepresentation by staff, who think he is being aggressive and trying to get them to work harder for less pay, and by corporations setting impossible targets."
He compared job security in the profession to that of football managers. "If you are not doing well in the league tables then you are out."
Southampton City College is now in the hands of a management team. A spokesman refused to give reasons for Dr Lavery's suspension, but denied reports that they were investigating allegations of financial mismanagement.
Dr Lavery, described by one colleague as a dedicated "elder statesman" of FE, has been head of the college for the past three years, and is the latest principal to be deposed in a spate of college power struggles. In the past 12 months principals at six colleges have been suspended or sacked.
Bernard Smith, a former principal, says the APC will be lobbying Gillian Shephard, the Education and Employment Secretary, and the FEFC for increased training for college governors. While some governing bodies were performing well, others had made their principals scapegoats, he said.
"We had very experienced chief education officers and education committees with years of experience. We are only three years into incorporation and a significant minority of governors really haven't got it sussed yet."