Two more crates of whisky, along with two of brandy, were also discovered but they were left under the floorboards of the hut.
The whisky is believed to have been bottled in Scotland in 1896 or 1897, making it among the oldest in the world.
Richard Paterson, Whyte and Mackay's master blender, said the analysis would be "for the benefit of the whisky industry".
"Never in the history of our industry have we had a century-old bottle of whisky stored in a natural fridge and subjected to some of the harshest conditions on this planet," he said.
"It is an absolute honour to be able to use my experience to analyse this amazing spirit."
For the next six weeks, the whisky will be analysed, nosed, and tasted in full laboratory conditions.
The Antarctic Heritage Trust shipped the crate to Canterbury Museum in Christchurch, New Zealand, where it was painstakingly thawed in controlled conditions, allowing historians to get to the bottles inside.
The bottles are so rare and valuable that Whyte and Mackay's owner Vijay Mallya personally collected them and flew them back to Scotland.