Strasbourg has ruled that the practice was a breach of human rights, but said no compensation or costs should be paid.
The UK Government is the subject of the case, and Westminster has been staunch in its denial of Strasbourg on the issue.
Scottish ministers have refused to accept denying inmates the vote was wrong.
"The Scottish Government's long-standing position is that we do not think prisoners should be given the right to vote," a spokesman said yesterday.
"In terms of the referendum, under the Scottish Independence Referendum (Franchise) Act 2013, convicted prisoners currently serving a custodial sentence will not be able to vote in the referendum."
Isabella Sankey of human rights group Liberty said: "While some Conservatives play cheap politics with Churchill's human rights legacy, the court urges the Government to listen to its own cross-party parliamentary committee and remove the blanket ban on prisoner voting.
"Despite a violation of almost 10 years, the court has shown patience and respect for parliamentary sovereignty - even now declining to award damages or costs."
The case before the European Court of Human Rights (ECHR) concerned 10 prisoners who were unable to vote in elections to the European Parliament on June 4 2009.
They are Paul Firth, Douglas Neil, Michael McKenna, Jamie Bain, Stewart McKechnie, David McConachie, Paul Dillon, Robert Dow, Raymond Lee and Raymond Lovie.
The ECHR ruled there had been a violation of Article 3 of the European Convention on Human Rights, right to a free election.
Judges said they reached this conclusion as the case was identical to another prisoner voting case in the UK, in which the blanket ban was deemed a breach.
The court rejected the applicants' claim for compensation and legal costs.
The judges said they recognised recent steps taken in the UK with the publication of a draft bill and the report of the Joint Committee on Prisoner Voting Rights appointed to examine the bill, which came back with a key recommendation to allow prisoners who were serving 12 months or less to be eligible to vote.
Because the legislation remained unamended, the court concluded there had been a violation of the convention.
However, the UK Government has escaped the prospect of having to make pay-outs in hundreds of similar cases before the ECHR in light of the ruling on compensation and legal costs.
A Ministry of Justice spokesman said: "The Government has always been clear that it believes prisoner voting is an issue that should ultimately be decided in the UK. The Government is reflecting on the report from the Joint Committee on Prisoner Voting Rights and is actively considering its recommendations.
"This is not a straightforward issue and the Government needs to think carefully about the recommendations, which included new options for implementation."
In 2005, the ECHR in Strasbourg ruled that the UK's ban on prisoners voting was unlawful following a claim made by convicted killer John Hirst.
But in 2011 MPs voted by 234 to 22 to preserve the ban, in spite of the ECHR ruling.