Union leaders claimed that many institutions across the country resembled "ghost towns" as their members joined picket lines.
Picket lines formed outside university buildings in Edinburgh, Glasgow, Aberdeen and Dundee.
But the Universities and Colleges Employers Association (UCEA), which represents and negotiates on behalf of institutions and has expressed "disappointment'' at the move, said the early indications were that the strike was having minimal impact.
The strike, by the University and College Union (UCU), Unison and Unite, centres on a 1% pay rise offered to university staff - including lecturers, technicians and administration workers - which the unions insist means there has been a 13% pay cut in real terms since October 2008.
The walkout is affecting 149 universities across the UK, according to the unions, with support services such as catering, cleaning and security hit alongside academic departments.
The three unions have said that between them, there will be tens of thousands of people taking part in the walkout.
Unison said that the action had garnered widespread support from staff and students, causing "major disruption" in 21 towns and cities across the UK, with classes cancelled and libraries, sports centres, food courts and swimming pools closed.
Unison general secretary Dave Prentis said: "Our members in higher education deserve a better standard of living for their hard work and the contribution they make to the success of UK universities."
UCU general secretary Sally Hunt said: "Staff, from porters to professors, have walked out this morning in protest at some of the most sustained pay cuts since the Second World War. Nobody wants to be on strike, but a 13% real-terms pay cut as vice-chancellors' pay continued to increase and universities' surpluses built up simply is not fair.
"Although still early, we are already hearing news of closed departments and buildings with some universities' entire teaching cancelled for the day. If the employers try to spin the action as having little impact, then it merely shows how out of touch they are with what is really happening on the ground at universities.
UCEA said that on top of the 1% general pay rise, many university staff get other contributions that will increase pay by 3% overall.
A spokesman said: "Institutions tell us that the vast majority of staff understand the reality of the current financial situation and do not support action which would harm their institutions, and especially their students.
"Today's action is passing off with only minimal disruption but since fewer than 5% of staff voted to support this strike, this was not surprising. Nonetheless, we are all disappointed that, after six months of extended talks and what we believe is a fair pay offer, these trade unions remain on a path to cause disruption."
UCEA said that according to the latest data available to them, 378,250 people work in the sector and of these 29,538, or 7.8%, voted from the three unions. Around 17,800 voted in favour of strike action.