The SWA took action against the proposal, which it said would breach European law, after it was passed by MSPs (members of the Scottish Parliament).
A Court of Session ruling dismissed the action and said plans to introduce 50p per unit minimum pricing were legal.
Gavin Hewitt, chief executive of the Scotch Whisky Association, said: “We are disappointed our petition for judicial review has been refused. We are surprised at the ruling in light of 30 years of European case law on minimum unit pricing (MUP). We will be appealing against this decision and we remain confident of our position.
“The view from Europe is very different to that expressed by the court and we are not alone in having concerns about the legality of MUP. We are joined in our legal action by spiritsEUROPE and Comite Vins. The European Commission and more than 10 member states have expressed their concerns that MUP contravenes European Union trading rules and their opposition to the Scottish proposals,” he said.
“We have consistently opposed MUP so our decision to appeal should not come as a surprise. The Scottish Government has agreed to not introduce MUP until the legal process, including appeals, is complete,” said Hewitt.