The decision was made against Austria, France and Ireland, where minimum pricing had been set on tobacco - partly on health reasons.
The SNP wants to adopt the measure in an effort to improve Scotland’s damaging relationship with drink.
Health Secretary Nicola Sturgeon said it is "inappropriate and irrelevant" to compare other countries’ laws on tobacco with the alcohol pricing plan.
But opponents of the scheme in the alcohol industry and in Holyrood called for a rethink.
Gavin Hewitt, chief executive of the Scotch Whisky Association, said: "The Scottish Government must recognise the legal situation and drop this proposal which would be hugely damaging to Scottish jobs."
Jeremy Beadles, chief executive of the Wine and Spirits Trade Association, said the European judgment left “no room for doubt” that "health reasons cannot be used to justify minimum pricing".
Government-backed academic research last month suggested that a minimum price for alcohol could help to save the nation almost £1 billion.
Ministers have not yet said what the proposed minimum price will be but 40p per unit has been used as an illustration.
This figure, coupled with a ban on promotions, could see alcohol-related deaths fall by about 70 in the first year of the policy, then by about 365 after 10 years, according to the Sheffield University study.
But opposition MSPs said the European ruling casts the scheme into doubt.
Labour health spokeswoman Cathy Jamieson said: "The Scottish Government needs to make clear if the legal opinion they have has been superseded by the ruling by the European Court's Advocate General.
"Alcohol is a problem in Scotland and that`s why Labour has called for a national consensus to tackle our hard-drinking culture involving all of our political parties, health organisations, the police and the industry itself."
Liberal Democrat justice spokesman Robert Brown said: "If they are still determined to press ahead with minimum pricing then they must make sure that it is at least legal."
Tory deputy leader Murdo Fraser said the ruling was a "hammer blow" to the SNP`s plan.
He added: "Blanket minimum pricing penalises responsible drinkers, damages the Scotch whisky industry and does nothing to tackle the root of the problem."
Ms Sturgeon said the scheme would tackle cheap alcohol favoured by problem drinkers.
She said: "It is entirely inappropriate and irrelevant to translate an opinion on tobacco to the totally different issue of minimum pricing of alcoholic products per unit of alcohol for public health reasons."
Ms Sturgeon said the European Commission had already said community legislation does not prohibit minimum pricing for alcohol on public health grounds.
She added: "The issue here is ending a situation where three-litre bottles of chemical cider are sold for £3, or 700ml bottles of industrial vodka for less than £7.
"These are the products favoured by problem drinkers and are exactly the ones that will be targeted by minimum pricing - not quality products sold at responsible prices."
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