At least six people were killed and around 190 injured, including 137 security forces, in fierce clashes as police tried to disperse the demonstration.
In Karachi, people supporting the sit-in took to the streets and blocked several roads, causing disruption in traffic flow.
"Pakistan's government called on the powerful military to deploy in the capital Islamabad overnight after deadly unrest broke out when police moved to dislodge an Islamist protest that has brought the city to a near-standstill".
Roughly 8,500 elite police and paramilitary troops in riot gear took part in the clearance operation, which was launched soon after the final deadline of 7 a.m. given to protesters expired.
Protesters had been blocking a key road connecting Islamabad and the neighboring city of Rawalpindi since November 6.
Television news channels remained off-air across the country under government orders on Sunday, as the country's media regulator said live coverage of the protest was hindering security operations.
"The Pakistani government has chose to summon army forces to country's capital Islamabad to establish order in the city following weeks of unrest caused by protesters opposing an amendment to election act, according to a statement issued on Saturday night".
Seemingly emboldened by the failure of the government to clear the protests, which have almost paralysed the capital, Khadim Hussain Rizvi - the firebrand cleric who leads the Tehreek-e Labbaik Pakistan party - has called for protesters to bring the whole country to a halt.
The meeting was also attended by the Punjab Chief Minister Shahbaz Sharif and Interior Minister Ahsan Iqbal.
"Seven of our prison vans, four small vehicles and a water tanker have been torched by the protesters", said a spokesperson for Rawalpindi police. "[There were] several thousands of agitators in some locations of the city, where they lit up branches to block the roads", a local reporter, Kiran Nazish, was quoted as saying by the Guardian.
But the confrontation quickly turned violent as security forces fired teargas and rubber bullets and the protesters tore through the streets setting fire to police cars.
Local hospitals reported that most of the injured were police officers, and that five civilians arrived dead from gunshot wounds.
"After almost three weeks of simmering tensions, a 20-day protest finally erupted in violence in the Pakistani capital of Islamabad".
"Only Allah is running this country", he added, complaining that the only channel working was Pakistan state TV - and it was airing a children's programme.
The group is demanding the resignation of the country's law minister for what it considers blasphemy after amended parliamentary bills weakened rules that require lawmakers to reference the Prophet Mohammed when taking their oaths. The religious groups protesting belonged to the Barelvi sect of Islam that has strong ties to Sufism. Hamid and his family weren't home at the time.
The amendment was deemed a "clerical error" by the government and was rectified.