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"The chief executive shall appoint a date, not later than 90 days before the expiry of the three year period for holding general elections to the federal and provincial assemblies and the senate of Pakistan," the 12-member bench said in a unanimous judgment.
But Hinna Jilani, secretary-general of the Pakistan Human Rights Commission, said the decision indicated how far the independence of the judiciary was in doubt.
In a BBC interview she said the ruling reinforced the view that the judiciary was failing Pakistan's constitution.
General Musharraf has so far refused to give a timetable for restoring democracy- although he may draw some comfort from the fact that the court did validate the army's decision to mount a coup.
The Pakistan Muslim League of ousted premier Nawaz Sharif had pleaded with the court to declare the takeover illegal, and restore the constitution and parliament as well as the ousted government.
Timetable
Members of the former government are nevertheless likely to be relieved that for the first time, a major state institution has given a specific timetable for restoring democracy.
Nawaz Sharif's former law minister, Khalid Anwar, argued that the three years should be treated as an outside time limit and that elections should be held straight away.
The court ruled that the coup was justified because of corruption and misrule and the bad shape of the economy at the time.
The military government had responded to the case against it by saying its actions had popular backing and were legal under a provisional constitutional order.
The order had been put in place by Pakistan's military ruler, General Pervez Musharraf, to provide emergency legal backing to his regime.
The BBC's Owen Bennett-Jones in Islamabad says the court ruling is unlikely to be welcomed by government lawyers who had argued that it was not possible to give a specific timetable for the restoration of democracy.
Faltering economy
General Musharraf has said he wants to tackle corruption and restore the faltering economy before arranging any handover to civilian rule.
Nawaz Sharif was overthrown after he tried to sack General Musharraf as army chief, and allegedly prevented a commercial airliner carrying the general and 198 other passengers from landing in Pakistan.
The plane eventually landed after the army took control of Karachi airport. General Musharraf subsequently declared himself chief executive and arrested Mr Sharif.
The ousted prime minister was last month convicted of hijacking and terrorism, and sentenced to life imprisonment.
He is currently being tried on separate corruption charges.