The defence had objected to the formation of the three-member special court saying that being the former army chief, 70-year-old Musharraf can only be tried by a military court.
The special court, headed by Justice Faisal Arab, had reserved its verdict for today on February 18.
The court dismissed Musharraf's petition saying it has the mandate to try him and adjourned the matter till March 4.
It also summoned Musharraf to appear before it on March 11.
Musharraf faces treason charges for suspending, subverting and abrogating the Constitution, imposing an emergency and detaining judges of the superior courts.
If convicted, he could face life imprisonment or the death penalty.
"He had signed the order (imposition of emergency) as the Army chief and not as President. The judges should have recused themselves as they are biased against Musharraf. They were dismissed by Musharraf and held agitations against him," one of Musharraf's lawyers Ahmed Raza Kasuri told reporters.
He alleged that facts and laws were "twisted".
Earlier, Rana Ijaz Ahmed, another lawyer of Musharraf, accused the judges of acting like "rented killers" when the judgement was read out.
Asked if this is how a lawyer should behave, Kasuri said, "Every person reacts in a different way to a situation. We were also there but didn't react in such a manner".
This is the first time in Pakistan's history that a former military chief is facing trial for treason.
Even though Musharraf had appeared before the court during the last hearing, it could not carry forward the proceedings as his lawyers had asked the court to decide on their applications against its mandate first.
After skipping numerous hearings, Musharraf was driven to the court in a motorcade from the Armed Forces Institute of Cardiology, Rawalpindi amidst tight security on February 18.
His 17-vehicle cavalcade included a bullet-proof car, pilot vehicles and an ambulance. Over 400 personnel were also deployed at the court premises.
Musharraf had taken ill and was rushed to the AFIC on January 2 when he was being transported under heavy guard to the special court. He has since been admitted in the hospital.
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