The move was rejected after a final debate on Scotland's Alcohol Bill last week.
BMA Scotland chairman Dr Brian Keighley said: 'This is a missed opportunity for our parliamentarians who had a real opportunity to drive forward public health policy, not just in Scotland but in the rest of the world.
'All politicians acknowledge that price is a significant factor in the level of alcohol consumption, so it is particularly disappointing that opponents voted down minimum pricing but did not propose any credible alternative.'
The BMA published a letter before the debate, signed by 165 people from leading organisations, urging politicians to 'put party politics to one side and make a positive choice for Scotland by backing minimum pricing of alcohol'.
NICE guidance published earlier this year recommended a minimum price for alcohol to tackle dangerous drinking (GP, 2 June 2010).
The NHS spends more than £2 billion a year treating the effects of alcohol abuse.