A night curfew was imposed on Khartoum following the violence, in which when thousands of people, some wielding knives and guns, took to the streets after news of Mr Garang’s death in a helicopter crash was confirmed.
Gunfire could be heard and witnesses saw several people lying wounded, some possibly dead, and cars set ablaze.
“We have received 26 bodies,” said a spokesman for the morgue at Khartoum’s general teaching hospital.
Sudan TV later broadcast a statement by the Sudan People’s Liberation Movement/Army (SPLM/A) which stressed Mr Garang’s death was “an accident, contrary to rumours giving other reasons to the death,” urging SPLM followers to observe self-restraint.
Deng Macham, a senior Dinka Sultan in Khartoum, also addressed southerners on television urging them to take seriously what the SPLM said.
“Don’t believe those who tell you that John Garang was killed by Mondokuru (northerners). He died in an accident,” said Mr Macham.
Meanwhile, residents of the southern town of Juba, which is to become the capital of the southern region, said protesters had burned and vandalised businesses owned by northern Sudanese Arabs.
They are seen as close to the Islamic government in Khartoum against which the SPLM had until January fought for 21 years, in Africa’s longest running war.
The SPLM has confirmed Mr Garang’s body will be buried in Juba, however gave no details of when the funeral will be held.
Sudanese President Omar el-Beshir earlier confirmed Mr Garang had died en route from Uganda to his base in southern Sudan when the Ugandan Russian-built helicopter in which he was travelling crashed near the Ugandan border.
Six people accompanying Mr Garang, and seven Ugandan crew members were also killed in the crash, which Ugandan officials blamed on poor weather.
Mr Garang had been returning after talks with Ugandan President Yoweri Museveni and US and European diplomats about the progress in implementing the January 9 peace deal.
Mr Garang became VP three weeks ago when the January peace agreement signed in Kenya came into force with the formation of a new national unity government.
His death sparked immediate concerns for the agreement as well as for peaceful resolutions to conflicts in Sudan’s troubled western Darfur region and the restive east of the country.
The SPLM said it had elected its number two, General Salva Kiir, as successor to Mr Garang.