The SWA and its ally in the battle, Spirits Europe, welcomed the news after arguing for years that MUP breaks EU law.
SWA chief executive David Frost said: “We are pleased that the Court of Session in Edinburgh is referring the MUP case to the Court of Justice of the European Union. From the outset we said that we believed MUP was contrary to European Union law and that it was likely in the end to go to the European Court.
“We also believe MUP would be ineffective in tackling alcohol misuse and would damage the Scotch Whisky industry in the UK and overseas.”
Paul Skehan, director general of Spirits Europe, added : “We welcome this decision. We have called for MUP to be referred to the Court of Justice of the European Union ECJ from the outset, believing that the question of its legality would always have to be decided there.
"Whatever about the legality of MUP, we have always contested the likely efficacy of the measure. Therefore, in advances of the ECJ hearing, we will continue to work with all willing partners to develop and support campaigns aimed at really reducing alcohol-related harm."
The Alcohol (Minimum Pricing) (Scotland) Act 2012 was passed by Holyrood in June 2012 and a minimum price of 50p per unit of alcohol was due to be implemented, but it has been delayed while appeals are processed.
The SWA's legal bid was rejected by Lord Doherty in May 2013 following an Outer House hearing in the Court of Session in January 2013.
An appeal to the court's Inner House, heard by Lord Eassie, Lord Menzies and Lord Brodie, took place in February.
Lord Easie said today: “There are thus aspects to the Scottish Ministers claim of justification under Article 36 TFEU upon which we consider that it would be of help to have the guidance of the Court of Justice of the European Union.”
It will now take several months before the case is heard in Luxembourg, and the health lobby in Scotland has accused the SWA of “costing lives” by delaying MUP with appeals.
Dr Evelyn Gillan, chief executive of Alcohol Focus Scotland, said: "If the appeal judges feel that clarification is needed on technical matters then we can only hope that this process does not drag on.
"Every week that minimum pricing is delayed, another 20 Scots lose their lives because of alcohol.
"It is frustrating to see a policy that has been agreed through the democratic process being held up by big business, who care more about protecting profits than the health and well-being of the people of Scotland."
Health secretary Alex Neil added: “While it is regrettable that this means we will not be able to implement minimum unit pricing sooner, we will continue our ongoing and productive dialogue with EU officials.”