Xinjiang's police chief was also fired from his post on Saturday, the Xinhua news agency reported.
Liu Yaohua was replaced by Zhu Changjie, the party chief of Xinjiang's Aksu area.
The sackings could feed more speculation about the future of Wang Lequan, the regional Communist party boss, who has barely appeared in state media in the past couple of days, after he pleaded from a balcony with crowds of Han Chinese demanding he be removed from his position.
Protesters accuse the authorities of failing to stop a number of syringe attacks or to punish the Muslim Uighurs they blame for the incidents.
But Uighur leaders say members of their community have also been hurt.
Security remains tight while signs of normality return to Urumqi. Soldiers were deployed at barricades on the city's streets on Saturday at a site where they fired tear gas on marching protesters the day before.
Melissa Chan, Al Jazeera's correspondent, reporting from Beijing, said: "The majority of the people on the streets in the centre of the city are the troops ... we still have to wait and see if the Chinese citizens have decided today whether they will gather once again to protest their grievances."
Zhang Hong, Urumqi's deputy mayor, said the deaths followed demonstrations on Thursday by ethnic Han Chinese demanding punishment of Muslim Uighurs blamed for the July 5 rioting that killed nearly 200 people.
"On Thursday, 14 people were injured and sent to hospital and five people were killed in the incidents, including two innocent people," Zhang said.
He did not say what he meant by "innocent" and gave no breakdown of the toll.
Protesters marched again on Friday, and police used tear gas and public appeals to break up crowds of Han who tried to break through to government offices.
There were no deaths in those protests, Zhang said.
Troops have filled the streets and blocked access to Uighur neighbourhoods in an attempt to quell further trouble.
"The riots and protests came as a huge embarrassment to the Chinese government," Ying Chan, the director of journalism and media studies at the University of Hong Kong, told Al Jazeera.
"Because just last week President Hu Jintao spent four days in Xinjiang, his first visit there since July. And earlier this week, the state news agency said the situation was stabilising and tourism coming back."
Xinjiang is officially an autonomous region but in practice it is tightly controlled by Beijing. It is sparsely populated but has large reserves of oil, gas and minerals.
The region's Turkic-speaking Uighur population number around eight million.
Uighur activists say migration from other parts of China is part of official effort to dilute and suppress Uighur culture in their own land.
China says Uighur separatists are terrorists and linked to al-Qaeda.
Uighur separatists have staged series of low-level attacks since early 1990s.