Police and paramilitary forces pulled back from an operation to break up a huge sit-in that had paralysed Islamabad for weeks after their clearance operation on Saturday turned deadly.
They were met with stubborn resistance by protesters who torched vehicles and threw stones.
The Interior Ministry did not specify when the troops would be deployed, and no soldiers were visible on the streets late Saturday.
The country's media regulator prohibited television channels from airing live images from the protest sites in order to minimise the impact of demonstrations.
In response to the government's request for assistance with the operation, the Army - in an official letter to the Interior Ministry - said that it was prepared to cooperate with security personnel in keeping with Article 245 of the Constitution to protect the life and property of the residents of Rawalpindi and Islamabad.
Last week, the Islamabad High Court ordered the government to clear the protest as they were causing a huge inconvenience to commuters between Islamabad and its twin city of Rawalpindi.
On Friday, the IHC, displeased with government inaction against the Faizabad protesters, had pointed out that the participants of the sit-in could be dispersed using options other than bullets.
Police on November 25 fought running battles with the Islamists, who are demanding the resignation of Pakistani Law Minister Zahid Hamidover over what they claim was a blasphemous parliamentary bill to amend the country's election laws.
Saturday's unrest in Islambad had spilled into cities across the country, including Karachi where roads were blocked and demonstrations were held. But witnesses said at one point a police van came under attack and was set on fire after two police officers aimed assault rifles at protesters. Protesters had camped at a busy intersection for days.
Police have confirmed that at least two protesters are dead.
Numerous protesters were armed with sticks or metal rods, and some held riot shields snatched from the police during the unsuccessful operation to clear the area.
Police lobbed tear gas canisters and deployed the water cannon while surrounding and arresting dozens of protesters who resisted by throwing rocks. More than 20 injured were taken to other hospitals.
The protesters, Iqbal added, had themselves fired teargas, usually the weapon of choice of most riot-control forces, at policemen trying to quell violence that has spread to cities, including Karachi, Lahore, Rawalpindi and Peshawar. In Lahore, an estimated 3,400 were occupying main roads.
Separately, Pakistan's telecom authority also banned access to social media networks like Twitter, YouTube, and Dailymotion in an attempt to prevent coverage of the standoff between the Islamist protesters and authorities.