Judge Lord Bracadale ruled that none of a series of challenges mounted by Imperial on the legislative competence of Holyrood to pass the measures was "well-founded".
The manufacturer had raised a judicial review at the Court of Session in Edinburgh, seeking a ruling that the prohibitions were outside the competence of the Scottish Parliament, and not law.
However, Bracadale ruled that the new offence of displaying cigarettes in shops did "not prevent a sale being made nor did it affect the terms of sale between the business selling tobacco products and the consumer purchasing them."
He also rejected Imperial's contention that the new provisions modified freedom of trade provisions set out in Article VI of the Act of Union.
It is now highly likely that the ban will be enforced in large stores from October 2011 and small stores in 2013, although exactly what form it will take is still being discussed by MPs.
The Scottish Grocers' Federation said it was bitterly disappointed by the outcome.