The National Association of Teachers in Further and Higher Education (Natfhe), and the Association of University Teachers (AUT), were joined by Unison and Amicus support staff.
Their protest was over the 10-year freeze in the London weighting of £2,134 for staff at London University, and subsidies of between £603 and £2,355 in the "new universities", the former polytechnics. The University of London has offered no automatic increase while vice-chancellors at the new universities have offered a £90 rise.
The unions said 120,000 students were affected by the strike. Paul Mackney, general secretary of Natfhe, said: "Today has been a warning to employers and the government that those who work in universities will not put up with underfunding and neglect."
He also promised a united front with the National Union of Students against top-up fees. The NUS has backed the strike.
Sally Hunt, general secretary of the AUT, said: "Pay for university staff in London is so low that, for many, buying a house is an impossibility. The last time London weighting was increased the end of the cold war had just been announced. That is simply unacceptable."
University staff receive less London weighting than the police, who get £6,111; the prison service, £3,500; and teachers, £3,105.
The Universities and Colleges Employers Association (UCEA) warned the strike would have "detrimental effects on students and research". Allowances for University of London staff are not covered by national negotiations.
Jocelyn Prudence, chief executive of the UCEA, said: "We are not unsympathetic. We know it costs a lot to live in London. But there is simply not the money to fund such a claim." She added: "The differing arrangements and levels of London allowances for higher education staff make for a necessarily complex picture."
"The issues would be best addressed in our negotiations with the unions about fundamental reform of pay arrangements for higher education."
Strikers picketed outside King's College London yesterday afternoon as the Queen arrived to open its new Maughan Library.
· The Association of Teachers and Lecturers, the most moderate of the three main teacher unions, yesterday voted against joining the National Union of Teachers and National Association of Schoolmasters/Union of Women Teachers in a one-day strike over London allowances.
