A further $1 million is expected to be raised from a new version of the $200-a-bottle spirit called The Journey.
"I was delighted when I heard Whyte & Mackay would launch a different product as the first edition went down particularly well," Nigel Watson, the trust's chief executive, said. "Not only will it give more people a chance to taste a part of history, the donation of future sales will greatly assist our efforts to conserve and maintain Shackleton's Antarctic legacy ."
The three original bottles of malt were flown to Scotland in 2011 on a private jet for testing, handcuffed to the wrist of Whyte & Mackay's master blender Richard Paterson.
The original bottles of whisky were returned to New Zealand last month intact, except for one small vial which Paterson keeps close to his heart.
"It is a wonderful reminder of what a historic whisky this is and of the men who, with Shackleton, really suffered in their endeavours to conquer the South Pole," Paterson said.