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.
Security forces fired tear gas and rubber bullets at the demonstrators but were met by stubborn resistance by protesters who blocked roads and torched vehicles around the site of the sit-in.
At least six people were killed and around 190 injured before security forces retreated on Saturday.
An interior ministry order said the federal government had authorised the deployment of "sufficient troops" to "control law and order" in the capital until further notice.
By daylight on Sunday there was no official military response and no sign of armoured vehicles or soldiers on the streets.
Private television broadcasts remained blocked and social media sites were restricted.
The little known Islamist group at the centre of the protest are demanding that Pakistan's law minister Zahid Hamid resign over a hastily-abandoned amendment to the oath that election candidates must swear.
Demonstrators have linked it to blasphemy -- a highly contentious issue in Muslim Pakistan -- and claim the oath was softened to enable the participation of Ahmadis, a long-persecuted Islamic minority sect.
Hundreds, possibly thousands, of demonstrators are believed to be still occupying roads and intersections connecting Islamabad with neighbouring Rawalpindi, with protesters posting videos late Saturday night of funeral prayers being recited at the sit-in.
The violent clashes spurred similar protests in major cities and towns nationwide.
Police in Karachi said some 200 protesters had blockaded a major road in the southern port, with at least 27 injured -- including 22 people with gunshot wounds -- brought to hospital, according to doctors.
Markets and shops were shuttered in the megacity, Pakistan's commercial hub, as alarmed residents stayed inside, while hardline clerics urged more people to take to the streets.
Analysts said the government had allowed a minor issue to grow into a headline-grabbing and potentially dangerous situation.