Wednesday's plea means Matthews maintains his innocence. It is a form of a guilty plea, but without an explicit admission of guilt.
Matthew, 33, of Charlottesville, also is charged in a separate case with the abduction and killing last year of University of Virginia student Hannah Graham.
His plea came after the prosecution rested its case with DNA evidence linking him to the September 2005 case in Fairfax. Defense lawyers tried unsuccessfully to get the judge to strike the case.
Prosecutor Ray Morrogh said Matthew is entering the plea without any plea agreement with prosecutors.
Matthew faces up to life in prison when sentenced Oct. 2.