Officials said the Red Mosque, or Lal Masjid, complex had been cleared of militants but troops were combing the area for booby traps and explosives.
The mosque's radical chief cleric, Abdul Rashid Ghazi, was among the dead, the army said.
The operation followed a week-long siege of the compound by troops.
The mosque had been the focus of spiralling tensions between the government and radical students, who had waged a campaign for the adoption of strict Islamic sharia law.
It had been feared that women and children might be among the casualties, but army spokesman Maj Gen Waheed Arshad said none had been found among the bodies.
Scores of civilians, and some militants, emerged from the complex after troops launched an all-out assault in the early hours of Tuesday morning.
Ten soldiers were killed in the fighting, which went from room-to-room.
Some 1,300 people managed to leave the compound during the stand-off, but at least 21 people, including an army commander, were killed.
It is not clear how many people were inside the complex when it was stormed.
Unexploded grenades
The BBC's Barbara Plett in Islamabad says the mosque is still off-limits and there is no independent story of what happened there.
Questions, such as how many people died, still need to be answered, our correspondent says.
The army says that will only be known after the clean-up operation.
"This whole area needs to be sanitised because we don't want unexploded grenades or mines or any other explosives lying around," said Gen Waheed.
The troops took control of the complex during the fighting, which lasted for some 36 hours.
Interior Ministry spokesman Javed Iqbal Cheema said Mr Ghazi was killed as troops were flushing out militants still inside a madrassa (religious school) for women and girls inside the compound.
Mr Ghazi's body was being sent to his home village in Baluchistan for burial.
Our correspondent says many Pakistanis supported the operation, saying the government had no choice but to confront the Islamic extremists.
But, she adds, the authorities fear a violent reaction from other radicals, and the country is on high alert.
Al-Qaeda's second-in-command, Ayman al-Zawahiri, issued a videotape calling on Pakistani Muslims to launch a "holy war".
In Karachi and Peshawar, near the Afghan border, where support for militants is rife, hundreds of angry demonstrators protested against the storming of the mosque.
Thousands of extra troops have been sent to the border area with Afghanistan amid fears of an Islamist backlash.
An opposition Islamic alliance, the Mutahida Majlis Amal, has declared three days of mourning in Pakistan's North West Frontier Province, the Associated Press news agency reported.
Meanwhile, pro-Taleban militants in the border tribal region of North Waziristan have told the government to withdraw troops from checkpoints or face renewed attacks.
"BBC Newspaper, Wednesday, 11 July 2007"
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