Mr. Musharraf’s lawyers had challenged the right of the civilian court in Islamabad to try the former army chief who appeared in person before judges for the first time on Tuesday.
“This application is dismissed,” lead judge Faisal Arab said at the end of Friday’s hearing.
The three-judge bench ruled that he was no longer in the army and that high treason can be tried exclusively in a special court.
“This decision to try Musharraf in a civilian court is factually wrong. The facts have been twisted,” Mr. Musharraf’s lawyer Ahmad Raza Kasuri told reporters afterwards.
Mr. Musharraf on Tuesday for the first time visited the court to face charges in a treason case. The 70-year-old arrived in a heavily protected cavalcade at the National Library in Islamabad where the court has been holding hearings, an AFP photographer had said.
No former military leader has appeared in court before and the trial is seen as a test of the supremacy of civilian rule in a country governed for more than half its history by the army after three coups.
Mr. Musharraf faces treason charges, which can carry the death penalty, over his suspension of the constitution and imposition of a state of emergency in 2007 while he was president.
He was first ordered before the tribunal on December 24 but had missed repeated hearings since then due to bomb scares and health issues that saw him complain of a heart problem.