Small stores had hoped that the charge of 45p per unit would help to level the field between themselves and their larger competitors.
Also rejected were proposals to give councils the power to ban the sale of alcohol to young adults under the age of 21 in areas where there is deemed to be a problem with alcohol abuse.
However, the Bill does signal and end to 'quantity discounts' such as 'three for two' offers. Alcohol advertising in or outside of stores will also be banned, while all licensed premises will have to introduce a Challenge 25 age-verification scheme.
Scottish Grocers Federation chief executive John Drummond said the legislation would herald increased costs for small stores, while doing "little to tackle the overconsumption of alcohol".
"Support for a ban on quantity discounts will not stop supermarkets from selling alcohol below cost. SGF will continue to lobby opposition parties to ensure the commitments made during the debate to work with Westminster to stop this irresponsible practice bear fruit," he added.
The new Bill will also pave the way for the introduction of a new 'social responsibility levy'. Under such a scheme businesses which profit from the sale of alcohol will be forced to pump money back into the community.
Licence-holders who comply with standards of practice in relation to social responsibility will be able to pay a discounted rate, but how this will be calculated is still unknown.