It was not clear whether the decision to hold prayers at the mosques was a change of policy or whether the mosques were opened because crowds had gathered outside.
One ethnic Uighur policeman guarding a mosque in the city told the Associated Press: "We decided to open the mosque because so many people had gathered. We did not want an incident."
According to Reuters news agency a small demonstration by Uighurs was broken up by Chinese riot police outside one mosque, but apart from the one isolated flare-up no other outbreaks of unrest were reported.
Thousands of Chinese troops using armoured cars and helicopters have been patrolling the city in a sweeping crackdown aimed at preventing further clashes between the Uighur and Han Chinese communities.
The move comes in the wake of ethnic violence that has left more than 150 people dead since Sunday in the region's worst ethnic violence in decades.
Al Jazeera's Melissa Chan, reporting from Urumqi, said the situation appeared to be back to normal on Friday although thousands of soldiers remained in the city, most of them stationed at mosques.
Our correspondent said state media continued to emphasise the importance of both Han Chinese and minorities working together, and commended soldiers for successfully bringing the situation under control.
Hu Jintao, the Chinese president, described the riots as a "serious violent crime elaborately planned and organised by 'three forces' at home and abroad", in reference to what China's government calls religious extremists, separatists and terrorists who they say menace Xinjiang.
Speaking at a Communist party conference, he said that officials and ordinary people "should cherish the great atmosphere of all the minorities working, preparing and developing together".
"We should bear this in mind that the Han people cannot be separated from minorities, and minorities cannot be separated from the Han people, and minorities are inseparable from each other either," Hu was quoted as saying in the local media.
|Urumqi's streets appeared relatively quiet on Friday after a week of deadly unrest [EPA]
Despite the authorities citing security fears that big Uighur gatherings could become another catalyst for unrest, the decision to silence congregational prayers could rankle the Uighurs, nearly all of whom are Muslims.
"Jumu'ah is the time of the week when we must pray. For us, it would be an insult to shut it down," said Ahmed Jan, a Uighur resident near the Dong Kuruk mosque.
"If we're not allowed to hold normal religious activities, there will be a lot of anger."
Xinjiang has long been a hotbed of ethnic tension, fostered by a growing economic gap between Uighurs and the Han Chinese, government curbs on religion and culture, as well as a massive influx of Han migrants who are now the majority in Urumqi.
On Tuesday, thousands of Han Chinese, vowing vengeance, attacked Uighur neighbourhoods, with many residents saying that people were killed, but the Chinese government has not released any figures beyond the 156 it says were killed in Sunday riots blamed on Uighurs.
Activists say the clashes started when armed police moved in to break up a peaceful demonstration called after two Uighur workers at a toy factory in southern China were killed in a clash with Han Chinese staff late last month.
The government has not revealed the ethnicities of the 156 nor given any information on more than 1,400 people it says were arrested in the wake of the clashes.
Xinjiang, a vast desert territory that borders Russia, Mongolia, Kazakhstan, Kyrgyzstan, Tajikistan, Afghanistan, Pakistan and India, has abundant oil reserves and is the country's largest natural gas-producing region.