The American tycoon had attempted to intervene in the case currently being considered by the Court of Sessions, but lord justice clerk, Lord Carloway ruled that Trump has no interest in the case and so cannot block the appeal.
Plans to construct the wind farm on the remote Islands were thrown into disarray in October following a judge's overturning of construction consent. Her ruling cited the lack of an electricity-generating licence and a failure to comply with an EU directive concerning rare birds.
If the Scottish government's appeal fails, there could be ramifications for other projects. It is standard practice to apply for an electricity generating licence only once a project has been been granted consent.
The initial judicial review was brought by anti-wind group Sustainable Shetland, but the group has distanced itself from association with Trump, saying it does not share his aims.
UK secretary of state for energy and climate change Ed Davey announced in only Septmember that a higher strike price would be paid for projects on remote Scottish islands to account for higher development costs.
The project is 50% owned by utility SSE. The other half is held by Viking Energy, which is 90% owned by community organisation Shetland Charitable Trust.
The Viking wind farm is a key part of Scotland's target of producing all of its domestic energy through renewables by 2020, and its collapse would be seen as a blow to this ambition.
The project would feature 103 turbines with a 3.6MW capacity. The Siemens 3.6MW is the most likely choice, but this has not been confirmed.
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