Kampala's rioting was triggered on Thursday by land and power disputes between the government and leaders of Buganda - one of the east African country's four ancient kingdoms.
Security forces on Thursday stopped a senior official from Buganda from going to the town of Kayunga to prepare for a visit by the king on Saturday, sparking the clashes in the capital.
Demonstrators threw stones and burned tyres while police, backed by the military, opened fire and sprayed tear gas to disperse the crowds.
Youths tried to erect barricades in the outlying Kubbiri and Kalerwe districts on Saturday, but security forces fired in the air and used tear gas to disperse them.
A torrential downpour in the afternoon cleared the streets.
Meanwhile, the leader of Uganda's largest ethnic group postponed a controversial visit to a rally in central Uganda in an effort to halt the deadly rioting.
Ronald Muwenda Mutebi, the traditional king, called off the trip to the town of Kayunga, scheduled for Saturday after the deaths, officials from Uganda's historical Buganda kingdom said.
"We don't want to see an escalation of the violence," Medard Lubega, the deputy information minister of Buganda, told the Reuters news agency.
The Ugandan government, citing fears of violence, had banned Mutebi from travelling to the region northeast of Kampala, an area on the edge of his jurisdiction as cultural leader.
The government's move sparked rioting from Mutebi's supporters in and around the capital and confrontations with security forces.
Yoweri Museveni, the Ugandan president, announced in a televised national address on Friday that his government would not give in and allow Mutebi into Kayunga county.
"I told him [the king] that the meeting in Kayunga will not take place until some conditions that will be communicated to him by the minister of internal affairs are met," Museveni said.
Buganda is one of the east African nation's four ancient kingdoms.
|A crowd of protesters surrounds a burning bus in Kampala on Friday [AFP]
It was abolished by Milton Obote, the former leader, in 1966 but restored by Museveni in the early 1990s.
Hassan Isilow, an independent journalist based in South Africa, told Al Jazeera, two issues were causing the problems.
"It’s about identity. The Baganda greatly associate with their king and believe the president of Uganda doesn't want to give them separate status," he said.
"The other issue is land. The government believes the king of the Baganda is going on a mobilisation tour telling his people about land issues.
"In 1966 a similar incident happened when the father of the current traditional leader was exiled to London. This time round we don’t think history will repeat itself, but these tensions are very high in Kampala."
The traditional Baganda king holds a largely ceremonial position in Uganda, but holds considerable influence among his people.
The Bagandas represent 6.4 million of Uganda's total population of 32 million, and they have advocated a federal system of government, which the administration of Museveni opposes.