Members of the AUT lecturers' union have voted to accept a new pay and job evaluation framework.
Employers say pay rises will be backdated
Industrial action, which was suspended at the AUT's conference last month, will now be called off permanently.
Employers at the "old" universities have welcomed the development, and say pay rises will be backdated to August.
The Educational Institute of Scotland (EIS) has also decided to accept the new agreement - so all the higher education unions have now done so.
The union said the vote, in a postal ballot, was 84.5% in favour of acceptance. A total of 22,238 members took part (52.1%).
The AUT (Association of University Teachers) said the agreement removed threatened losses of career earnings for many academic and related staff.
"If implemented properly, it should produce significant additional pay increases, targeted initially at those at the lower end of the pay scales."
The union's general secretary, Sally Hunt, said: "We will have to work hard with the employers to ensure that the national principles are implemented at pre-92 institutions and that we achieve pay harmonisation across the sector.
"The onus is now on the employers to deliver on the agreement."
She repeated that she deeply regretted any inconvenience caused to students.
Her members took part in a series of one-day strikes around the UK and boycotting assessment of students' work.
Most of the other unions have already accepted the new pay and conditions package.
The chief executive of the Universities and Colleges Employers Association, Jocelyn Prudence, said the vote was "extremely good news".
"Staff throughout the higher education sector will now be able to benefit from immediate pay increases and from the long-needed modernisation of pay structures."
The association said pay rises would be backdated to August 2003.
It said the two-year pay deal associated with the new framework provided an average 7.7% rise "and potentially more for many AUT members".
Members of the Educational Institute of Scotland (EIS) voted against accepting the agreement - but then also voted not to take industrial action.
The union's executive met on Friday to decide what to do next, and concluded that the vote against action was, in effect, a vote to accept the deal.
"The employers' association has been informed of this decision and a letter has been written to all EIS Lecturers to explain this decision and its implications," a spokesman said.
"So, in short, the effect is that the deal is now being accepted by EIS members."