The group left hours after the government threatened to use force to disperse them.
They were angry at last month's hanging of a policeman who had shot and killed a secular governor over his opposition to the country's strict blasphemy laws.
They had demanded strict Sharia law and the hanging of a Christian woman the governor had defended against blasphemy allegations.
Awais Noorani, one of the protest leaders, called on the demonstrators to disperse, saying a deal was reached with the government.
Noorul Haq Qadri, who said he had helped negotiate the deal on behalf of the protesters, said the government had given assurances that there would be no attempt to amend the blasphemy laws and that it would release all detained protesters who were not wanted on other charges.
However, a government minister, Chaudhry Nisar Ali Khan said this was a lie and none of the protestor's demands had been met.
Police have detained more than 1,000 protesters in the last four days and they would all face prosecution, he added.
The protests paralysed one of the busiest areas of Islamabad. Most of the businesses in the area and schools across the city remained closed.
More than 10,000 Islamists from Pakistan's Sunni Tehreek group descended on Islamabad on Sunday to denounce last month's hanging of officer Mumtaz Qadri for the 2011 murder of secular governor Salman Taseer.
Their rally turned violent and police fired tear gas on Sunday, but failed to disperse the protesters, who damaged bus stations, traffic lights and CCTV cameras. The sit-in continued, but the number of protesters had dwindled to about 1,200.
The protest comes against the backdrop of a massive suicide bombing by a breakaway Taliban faction that targeted Christians gathered for Easter Sunday in a park in Lahore, killing 72 people, mostly Muslims.
