Later on in the day, in a televised address to the nation, Ibn Auf announced that 75-year-old al-Bashir had been overthrown and taken to a "safe place" after being arrested.
"That's why demonstrators are calling for a complete overhaul of the government and a peaceful transfer of power to civilian authorities", he said.
A striking photo of one protester standing on a vehicle and wearing a white thoub, a long robe, and gold earrings as she urged on a crowd this week was called an iconic image of the demonstrations and was shared widely online.
Cape Town - Sudanese President Omar al-Bashir is set to step down, Al Arabiya is reporting. The country's state broadcaster was seized by the military in the morning.
Aside from the fact that they are all hard-working, extremely well educated and successful, the other thing they have in common is that they - or their families - all fled Sudan as a result of the 1985 overthrow of the Numairi regime, which was inspired by Islamist leader Hassan Al-Turabi, who for long was Al-Bashir's religious backer.
The protests in Sudan, compared with the unfurling and contemporaneous events in Algeria, have sparked Egyptians to reflect over the current political situation in the country as well as the future of Sudanese-Egyptians relations.
Kabore said coups are put on trial in a democratic system.
The crisis intensified on April 6 - the 34th anniversary of a non-violent uprising that removed ruler Jaafar Nimeiri - when thousands began amassing in front of the army headquarters.
"We will not stop our revolution". He also said al-Bashir's crackdown against protesters risked splitting the security establishment and "could cause grave casualties".
Mr Auf's announcement also appears to have divided the army.
Outside the sprawling complex, protesters beat drums, sang and chanted slogans such "Peace!"
But the festive mood later soured.
"We call on our people from across the Khartoum capital and the region around to immediately go to the sit-in area and not leave from there until our next statement is issued", the Sudanese Professionals Association said. They danced and shouted to celebrate.
It also urged the army to give executive powers to civilians.
Guterres appealed for "calm and utmost restraint by all".
The AU says the move is not the appropriate response to the challenges facing Sudan and the aspirations of its people.
Army vehicles carrying troops were seen deploying across the centre of Khartoum from early Thursday.
Bashir's ruling National Congress Party said plans to hold a rally backing the president on Thursday had been postponed.
In recent days, soldiers protected demonstrators from other security services that were attempting to disperse them. Also, Islamic judges were sent to the country's mainly animist, Christian south, fueling the civil war that was already going on for years.
He tightened his control by building up an array of competing security forces and militias, as well as the regular army.
Meanwhile, Sudan's feared National Intelligence and Security Service said it was freeing all the country's political prisoners, state media reported.
Sharan Grewal, a postdoctoral fellow at the Center for Middle East Policy at the Brookings Institution, said it was hard to predict whether the latest convulsions would trigger a repeat of the 2010-11 Arab Spring protests that ousted regimes in Egypt and Tunisia and led to war in Syria and Yemen.
The latest crisis has escalated since the weekend, when thousands of demonstrators began camping out outside the defense ministry compound, where Bashir's residence is located.
Government officials said 38 people had died since December but Human Rights Watch said the number was higher.