They were demanding justice for clansmen killed by a rival ethnic group over a land dispute in the southern Blue Nile state.
There were similar protests on Tuesday in several cities to the east and west of the capital.
Also on Tuesday, the Health Ministry in Khartoum raised to 105 the death toll from the violence in Blue Nile, up from the 79 it reported on Monday. It said another 246 were injured.
The UN said 17,300 people were displaced as a result of the violence, which broke out on July 12 between the Berti and Hausa tribes in Blue Nile.
On Monday, the violence spread to the city of Kassala in eastern Sudan, and Wad Madani in Al Jazeera state, south of Khartoum. At least three people were killed in Kassala.
The clashes in Blue Nile prompted authorities to impose a curfew on the state’s major cities Rosiris and Damazin, and to ban gatherings there and in Kassala.
The army and police sent reinforcements to maintain order.
On Tuesday, Hausa protesters in Khartoum held up signs demanding “justice for the Blue Nile martyrs” and “no to the murder of Hausas”.
Video footage shared online showed hundreds of protesters marching near the city centre as tear gas rained on them.
There were smaller demonstrations by the Hausas in Al Showak, in Gedaref state east of Khartoum, and in El Obeid, capital of North Kordofan state in western Sudan.
“The Hausa will win,” chanted the protesters in El Obeid.
On the Red Sea in Port Sudan, the country’s main sea outlet, hundreds gathered outside local government offices calling for justice for those killed.
Deadly clashes regularly erupt in Sudan over land, livestock, access to water and grazing lands, especially in areas still reeling from the impact of decades of civil war and still awash with weapons, such as Blue Nile, Darfur and South Kordofan.
Experts and pro-democracy activists say a military takeover, led by army chief Gen Abdel Fattah Al Burhan last October has created a security vacuum that allowed a resurgence in ethnic violence in Sudan’s outlying areas.
Guerrillas in Blue Nile battled government forces during the rule of ousted ruler Omar Al Bashir, as part of the 1983 to 2005 civil war in the south. They took up arms against the government again in 2011.
Al Bashir was ousted by his generals amid mass protests against his rule in 2019.
In 2020, a civilian-military power-sharing government reached a peace deal with key rebel groups, including from Blue Nile, as well as the war-ravaged Darfur region.
Pro-democracy activists have accused Sudan's military and ex-rebel leaders who signed that peace deal of exacerbating ethnic tensions for political gain, claims the ruling generals reject.
The Hausas are one of Africa’s largest ethnic groups, with tens of millions living in several countries.
There are three million Hausas in Sudan, most of whom are Muslims who speak their own native language, in addition to Arabic.
They mostly live off agriculture in Darfur, Al Jazeera state in central Sudan and in the eastern states of Kassala, Gedaref, Sennar and Blue Nile.
Democratic transition derailed
Sudan has since the military takeover been embroiled in a political crisis, with its democratic transition in tatters and its economy devastated by high energy prices, food shortages and the suspension by the West of billions of dollars of aid and debt forgiveness.
The country has also been steadily slipping back into the pariah status it suffered for most of the 29 years Al Bashir was in power.
The West has repeatedly protested against the killing of unarmed anti-military protesters at the hands of security forces since the October 25 coup.
At least 114 protesters have been killed and about 6,000 injured since the takeover.