Andrew Gillon and Leslie Moohan, and a third long-term prisoner Gary Gibson, challenged the blanket ban on convicted inmates taking part in the ballot on the country's future.
But Lord Glennie yesterday ruled that the judicial reviews brought by the trio, who are all prisoners in Addiewell jail in West Lothian, must be refused.
Gillon and Moohan are both serving life sentences imposed in 1998 and 2008 respectively after being convicted of committing murders and Gibson is serving a term of seven years and four months imposed on him last year.
Lord Glennie said: "None of the petitioners is due to be released until after the date fixed for the referendum. They will all still be serving prisoners at the time of the referendum."
They will be ineligible to vote under the terms of the Franchise Act for the referendum but each wants to cast a vote at the ballot box.
The trio claimed that the blanket ban on convicted prisoners voting in the poll was unlawful and incompatible with their rights under the European Convention on Human Rights (ECHR).
They also challenged the decision to exclude them from the franchise on the basis of constitutional rights such as the rule of law, right to vote and respect for international obligations.
They further claimed that where the result of the referendum would or might lead to the loss of European Union rights, the blanket ban was contrary to EU law. The ECHR has previously held a blanket ban on prisoners voting is unlawful.