It followed an appeal by the Scotch Whisky Association, which had argued the proposal breached European law.
Judge Lord Eassie said there was “uncertainty” about the proposal and that it would “be of help to have the guidance of the Court of Justice of the European Union”.
David Frost, SWA chief executive, said: "We are pleased that the Court of Session in Edinburgh is referring the minimum unit pricing (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."
The Scottish Government brought in legislation to implement minimum pricing two years ago but it has been subject to a series of legal challenges.
Scottish Health Secretary Alex Neil said he was "frustrated" by the latest delay but expressed determination to see it through.
Miles Beale, chief executive of the Wine and Spirits Trade Association, said: "The WSTA welcomes the decision by the Inner House of The Court of Session to refer the minimum unit pricing legal challenge directly to the European Court of Justice.
"We believe MUP is contrary to European law, ineffective and would punish responsible drinkers, and that the European Court of Justice is the most appropriate court to consider its legality.
"In the meantime the industry is committed to working in partnership with Government and others to support policies which are proven to tackle alcohol misuse effectively."