It rejected an appeal by David Chaytor, Elliot Morley and Jim Devine that their cases should be heard by Parliament, not the courts.
The three men, who all deny theft by false accounting, will face separate trials at Southwark Crown Court.
The Supreme Court said the reasons for rejecting the appeal would be given at a later date.
But the decision upholds a ruling by the Court of Appeal in July that the three were not protected by parliamentary privilege - an ancient right protecting MPs from legal action arising from proceedings in Parliament - in relation to their expenses claims.
Former Bury North MP Mr Chaytor, 61, of Todmorden, West Yorkshire; former Scunthorpe MP Mr Morley, 58, of Winterton, north Lincolnshire; and former Livingston MP Mr Devine, 57, of Bathgate, West Lothian, are all on unconditional bail and face separate trials. The first, Mr Morley's trial, is expected to begin on 22 November.
In the Supreme Court hearing last month, Nigel Pleming QC, representing two of the men, told a panel of nine Supreme Court Justices that their appeal was "not, and never has been, an attempt to take them above or outside the law".
He argued important issues of principle were raised by the case and the allegations had to be "dealt with by the correct law, the law of Parliament" - arguing that only Parliament could question and impugn statements made in Parliament.
He argued that the expenses scheme was created and is administered by Parliament for Parliamentarians: "The administration of the scheme is also entirely a matter for the House of Commons - this extends not only to its creation but to its regulation and enforcement."
But in a brief hearing on Wednesday, Supreme Court President Lord Phillips said: "Each of these appeals is dismissed. The reasons will be given later."
In July the Court of Appeal ruled that parliamentary immunity or privilege had never been attached to allegations MPs had committed "crimes of dishonesty".
All three men were barred by their party from standing again as Labour MPs at the general election.
The charges against them followed a nine-month police investigation triggered after details of all MPs' expenses claims were leaked to a national newspaper.
Three former Labour MPs should face criminal trials over their expenses claims, the Supreme Court has ruled.