The University and College Union has accepted the ?150 lump-sum offer for 2011-12 after an online ballot in which 57.3 per cent backed accepting it.
However, Unite has rejected the offer and will ballot its higher education members for industrial action.
Meanwhile, university employers are likely to see the triennial valuation of the Universities Superannuation Scheme - the pension fund for traditional universities - as ammunition in their battle against the UCU, which began industrial action in protest at cuts to benefits earlier this month.
The results, announced to institutions this week, are expected to show a worse-than-expected deficit of ?2.9 billion.
On pay, a deal on the ?150 offer would follow below-inflation increases of 0.4 per cent and 0.5 per cent in the past two years.
The sector's five unions had submitted a joint claim to keep this year's pay in line with retail prices index inflation, which currently stands at 5.6 per cent.
However, even for cleaners and porters on the lowest level of the national pay spine - which starts at ?13,203 a year - the ?150 lump sum would amount to a rise of just 1.1 per cent.
In addition to the conflicting stances of the UCU and Unite, Unison and the GMB are still considering the pay offer, while the Educational Institute of Scotland is set to accept following a survey of its members.
Mike Robinson, Unite's national education officer, said: "Inflation over the past three years has been 12.4 per cent, so in real terms the offers on pay equate to a pay cut of about 11 per cent."
Jocelyn Prudence, chief executive of the Universities and Colleges Employers Association, predicted at a seminar on 14 October that the unions would fight harder under higher fees from 2012-13, given their perception that universities would be flush with funds.
On pay talks, her presentation states: "Finish line in sight - current low-key approach as all eyes turning to 2012-13 - sector awash with cash..."
Jon Richards, Unison's national secretary for education and children's services, said the union's national committee meeting on 20 October would "review the success or otherwise of the dispute talks so far and the somewhat contrary positions of our sister unions".
He added: "Whatever happens we will be looking for a better deal next year when fees kick in."
A UCU spokesman said that as sector income is predicted to grow under the higher fees regime, "we will take that...into account when we develop our next pay claim."
A Ucea spokesman said the lump-sum offer was "in recognition of the difficulties faced by the lower-paid staff working in the sector in the current financial climate".