Members of the GMB union voted strongly in favour of the deal, but it was rejected by Unite members.
The dispute is over plans to move staff from a final salary pension scheme.
Both unions voted last month to take industrial action at Diageo sites in Scotland, as well as other locations in Northern Ireland and Cheshire.
A deal appeared to have been struck following further talks with the company.
Members of the GMB union, which has 1,200 members working with Diageo in Scotland, voted by almost 3-1 in favour of accepting the deal.
But Unite members rejected it by a margin of 62% to 38%.
Diageo, which is the world's largest producer of Scotch whisky, said it awaited confirmation from Unite of its position.
Unite, which has more than 700 members at Diageo sites around the UK, has yet to comment on the the outcome of its ballot.
However, it is understood union officials will be speaking to Unite representatives at Diageo in the coming days.
The GMB union's Scotland organiser, Louise Gilmour said: "After a long campaign our members have voted strongly to accept this deal which means they will continue to have a pension scheme that ranks among the very best in the UK private sector.
"We will now sit down with Diageo and talk about the future to ensure the interests of our members are at the very heart of this hugely profitable global company that is so vital to the Scottish economy."
In a statement, the company said it was committed to "providing competitive and sustainable pensions".
It said: "In the last decade we have invested an additional Â£1.1bn into the final salary scheme over and above our normal employer contributions.
"With the costs of this scheme escalating, it is simply no longer sustainable."
Diageo said it had held "extensive talks" since February with UK employees on proposed changes to the final salary scheme.
It added: "The GMB trade union membership, our majority union, has accepted the company proposal.
"The minority union membership, Unite, has rejected the proposal and we await confirmation of their position.
"We will seek to engage in discussions with the GMB trade union and other employee representative forums to move forward on this proposal."
In Scotland, Diageo runs 29 distilleries and two bottling plants at Leven in Fife and Shieldhall, Glasgow.
Its brands include Johnnie Walker, Bells, Talisker and Dalwhinnie.
Drinks giant Diageo could face industrial action after one of the two unions representing workers rejected a deal to end a dispute over pensions.