The main judgment was written by Justice Seth.
But if found dead beforehand, "his corpse (should) be dragged to D-Chowk, Islamabad, Pakistan, and be hanged for three days", it said.
The chowk, or square, is just outside parliament.
"I dissent with the President (.) it has no basis in law and will be ultra vires for this court to do so". His lawyers have said they will appeal the verdict.
In further embarrassment for Pakistan Prime Minister Imran Khan, the Council claimed that his government had been installed by the Army. He said the court verdict against him was questionable and that the supremacy of rule of law was not maintained.
His rule faced no serious challenges until he tried to sack the chief justice in March 2007, sparking nationwide protests and months of turmoil that led to the imposition of a state of emergency.
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"There is no question that a person who had committed treason must be punished but in this case the right of fair trial guaranteed under the Constitution was not ensured". But his arguments were turned down by the courts and he was accused of acting illegally. "We welcome this court ruling", Iqbal said, adding that the judges had done justice to a former dictator.
The verdict sent shudders through the military, which has ruled Pakistan for the a large portion of its history and remains highly influential.
The apex body of Pakistani lawyers has slammed the Army for criticising the judgement of the special court against Gen (retd) Pervez Musharraf in the treason case, terming it a clear cut violation of the legal and constitutional provisions which amounts to contempt of the court.
Following his sentencing on Tuesday, the Pakistan Army reacted angrily and said that its former chief can "never be a traitor".
The ISPR said that the armed forces still expected justice in line with the Constitution of Islamic Republic of Pakistan.
At that time, Musharraf held the presidency while also heading the country's military.
Musharraf served in the elite SSG from 1966-1972 and during the 1971 Pak-India war, he was a company commander of an SSG commando battalion.
Musharraf, who ruled Pakistan between 1999 and 2008, is the first military ruler to stand trial in Pakistan for overruling the constitution.
Former Pakistani president Pervez Musharraf is escorted by soldiers as he salutes on his arrival at an anti-terrorism court in Islamabad, 2013.