In a unanimous decision they rejected appeals brought by former Livingston MP Jim Devine, David Chaytor and Elliot Morley, who deny theft by false accounting and are facing separate trials.
In their challenge before the nine justices they all raised a common point of law - that criminal proceedings cannot be brought because they would infringe parliamentary privilege.
Their claim to privilege had two bases. The first related to Article 9 of the Bill of Rights 1689, which provides that the freedom of speech and debates or proceedings in Parliament "ought not to be impeached or questioned" in any court or place out of Parliament.
The second related to the "exclusive jurisdiction" of Parliament and referred to the right of each House to manage its own affairs without interference from the other or from outside Parliament.
But the justices, headed by the president Lord Phillips, held that neither Article 9 nor the exclusive jurisdiction of the House of Commons posed any bar to the jurisdiction of the Crown Court to try the former MPs.
The three took their cases to the highest court in the land claiming any investigation into their expenses claims and the imposition of any sanctions "should lie within the hands of Parliament".
During the hearing of the appeal in October, Nigel Pleming QC, representing Chaytor and Devine, told the justices that the parliamentary expenses scheme was part of proceedings in the House, so the men should be protected by parliamentary privilege.
He added: "I also wish to emphasise as firmly as I can on behalf of these former MPs that this is not, and never has been, an attempt to take them above or outside the law."
He said the House had "the power to punish, and to recover any monies wrongly claimed, and is well capable of investigating allegations, including allegations of dishonesty, made against its members".
The Lord Chief Justice, Lord Judge, heading a panel of three Court of Appeal judges, earlier this year upheld a ruling by a judge at Southwark Crown Court that the ex-MPs were not protected by privilege.
Former Bury North MP Chaytor, 61, of Todmorden, West Yorkshire; ex-Scunthorpe MP Morley, 58, of Winterton, north Lincolnshire; and Devine, 57, of Bathgate, West Lothian, are all on unconditional bail.
The issue under Article 9 was whether making claims for parliamentary expenses fell within the phrase "proceedings in Parliament".
The justices held that conduct of a member of Parliament is not privileged merely because it occurs within the House of Commons.
The principle matter to which Article 9 was directed was freedom of speech and debate in the Houses of Parliament and parliamentary committees.
Lord Phillips said: "In considering whether actions outside the House and committees fall within parliamentary proceedings because of their connection to them, it is necessary to consider the nature of that connection and whether, if such actions do not enjoy privilege, this is likely to impact adversely on the core or essential business of Parliament.
"If this approach is adopted, the submission of claim forms for allowances and expenses do not qualify for the protection of privilege.
"Scrutiny of claims by the courts will have no adverse impact on the core or essential business of Parliament, it will not inhibit debate or freedom of speech."
He added: "Indeed it will not inhibit any of the varied activities in which Members of Parliament indulge that bear in one way or another on their parliamentary duties.
"The only thing that it will inhibit is the making of dishonest claims."
Lord Phillips said: "Thus precedent, the views of Parliament and policy all point in the same direction. Submitting claims for allowances and expenses does not form part of, nor is it incidental to, the core or essential business of Parliament, which consists of collective deliberation and decision making.
"The submission of claims is an activity which is an incident of the administration of Parliament; it is not part of the proceedings of Parliament."
He said he was satisfied that Mr Justice Saunders and the Court of Appeal were "right to reject the defendants' reliance on Article 9."
Lord Phillips concluded that he was "satisfied" that "neither Article 9 nor the exclusive cognisance of the House of Commons poses any bar to the jurisdiction of the Crown Court to try these defendants".