Sapiov's father, Avaz Saipov, initiated the Supreme Court appeal, hoping that his son's murder would be reinvestigated by a different court.
But the Supreme Court's ruling means the same court will be conducting the fresh investigation.
Former policeman Abdufarid Rasulov has been accused of involvement in Saipov's murder and was awaiting trial.
Twenty-six-year-old Alisher Saipov, who was murdered in broad daylight in 2007, was an ethnic Uzbek and editor in chief of an Osh-based newspaper who often wrote articles critical of Uzbek President Islam Karimov and his government.
He also worked as a correspondent for RFE/RL and Voice of America.
In 2007 Saipov was shot dead as he left his office in central Osh.
His father told RFE/RL that he was unhappy with today's Supreme Court decision.
He insisted he has evidence that shows his son was killed by agents from Uzbekistan in retaliation for the critical articles he wrote.