refusing to bury the victims of Pakistan's worst single attack on Shiites, which killed 92 people in the southwestern city of Quetta last Thursday.
In other cities across Pakistan, solidarity protests were held by hundreds of other Shiites, who account for 20% of the population and according to Human Rights Watch last year suffered record levels of violence.
The protesters had demanded that the army take over in the southwestern province of Baluchistan, which also suffers from a nine-year separatist insurgency and Islamist militancy.
Extreme Sunni Muslim group Lashkar-e-Jhangvi claimed responsibility for Thursday's bombing at a snooker hall, which wounded more than 120 people.
Hazaras were initially divided over whether the government had gone far enough in accepting their demands by appointing the governor to take over, but by 11:00am (0600 GMT), families started leaving to prepare their dead for burial.
"The protest has been called off, burials will be after Zuhar (afternoon) prayers," Shiite leader Sadat Ali Khan announced at the protest.
An AFP photographer said families had started to take bodies of loved ones killed on Thursday to a local mosque to prepare them for burial.
Shiite leaders had said overnight that they would not call off their protest until they saw official notification of the orders from Prime Minister Raja Pervez Ashraf.
Ashraf flew to Quetta on Sunday to meet the protesters and announced live on television in the middle of the night that the provincial government would be sacked and the governor, appointed by the president in Islamabad, would take over.
He said governor Nawab Zulfiqar Magsi could call the army at "any time for assistance" and that the top military commander in Baluchistan would "directly" supervise paramilitary forces who have the power to arrest and investigate anyone.
"We are determined to defeat this mindset," Ashraf was quoted as saying by state media in reference to those he accused of trying to create a divide between Shiites and Sunnis.
"I have great respect for the sacrifice, tolerance and peaceful behaviour of the Hazara community. You are an asset of Pakistan," he added.
Refusing to bury the dead is an extreme protest in Islamic society, where the deceased are normally buried the same or next day.
The provincial government was widely criticised for being unable to control the myriad security problems in Baluchistan and the chief minister, Aslam Raisani, was criticised for making a trip to London while security deteriorated.
In Karachi, Pakistan's financial capital, authorities announced that they had suspended cell phone services "for a few hours because of security reasons" on Monday.
More than 1,000 people had gathered near President Asif Ali Zardari's house in the upmarket neighbourhood of Clifton late on Saturday in solidarity with the Hazaras and hundreds of them remained there until Monday morning.
"We are leaving now, as our demands have been accepted and our brothers in Quetta have asked us to end our protest," said participant Shaukat Ali