The Social Justice Party sought immunity for Musharraf under Constitutional provisions, contending that he could not be included in the investigation or declared an accused as he was President at the time of Bhutto's assassination.
Judge Chaudhry Habib-ur-Rehman of the anti-terrorism court in Rawalpindi dismissed the petition after hearing arguments by Federal Investigation Agency (FIA) Prosecutor Chaudhry Azhar, Pakistan Peoples Party lawyer Latif Khosa and Social Justice Party head Akhtar Shah.
Former premier Bhutto was killed by a suicide bomber shortly after addressing an election rally in Rawalpindi in December 2007. Musharraf has been accused of failing to provide security to her.
The court also dismissed Shah's request to become a party in the case, saying he was politically affiliated. The court ordered fresh trial in the case that will begin on October 22. It also summoned four prosecution witnesses.
The 70-year-old former army chief was arrested by FIA on April 26 and later granted bail in the case against two surety bonds of Rs 1 million each.