Ibn Auf had served as Bashir's defense minister right up to the president's downfall, after three decades of iron-fisted rule and was widely despised on the streets.
Sudan's Defence Minister Awad Ibn Auf has stepped down as leader of the new Military Transitional Council, he said, a day after ousting the president.
Political parties and movements behind the protests said they were meeting Saturday with the military to discuss the transition, saying they've formed a 10-member delegation to introduce the people's demands to the military council.
A military takeover has taken place in Sudan.
What followed was a series of protests by human activists groups.
Sudan's opposition Freedom and Change Alliance urged the new leadership of the Transitional Military Council to transfer power to a transitional civilian government on Friday, calling on the protesters to continue their sit-in before the army's general headquarters.
Washington, through state department spokesman Robert Palladino asked Khartoum to "exercise restraint and to allow space for civilian participation within the government".
Sudanese leader Omar al-Bashir was booted from power Thursday, following a week in which thousands of protesters camped out in the country's capital, Khartoum.
It did not announce any course of action or whether it would engage the coup leaders.
"The Sudanese people should determine who leads them and their future".
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The Transitional Military Council has promised that the new government will be composed of civilians. We have come with no ideology, we have come here to maintain order and security to provide the opportunity for the people of Sudan to achieve the change they aspire to. "We want a civilian leader".
The military council said on Thursday it expected a pre-election transition to last two years at most or less if chaos could be avoided.
The United Nations human rights office called on Sudan to cooperate with the International Criminal Court (ICC), which issued an arrest warrant for deposed Bashir for alleged war crimes almost 15 years ago. Mr Ibnauf, however, faces a similar predicament and has ruled out extraditing Mr Bashir.
They fear the military, which is dominated by Bashir loyalists, will rule indefinitely or hand power to one of its own. "We may try him, but we will not hand him over".
A United Nations mission in 2005 listed him among those responsible for the deteriorating situation in Darfur after which the USA blocked his assets in May 2007.
The military council also said it was declaring a ceasefire across the country, including in war-torn Darfur.
The announcement was the latest political drama to unfold in Sudan, where demonstrators have been protesting for months, demanding economic and political reforms.
"Omar al-Bashir is wanted for some of the most odious human rights violations of our generation and we need to finally see him held accountable", Mr Naidoo added.
"Any and all of their accomplices should be tried before competent national courts as part of a transitional justice process that must go hand-in-hand with a genuine transition to democracy", said Amir Suliman, Legal Programme Director, African Center for Justice and Peace Studies (ACJPS), Sudan. He also confirmed that top government members, including the vice-president and al-Bashir's associates, are under arrest but didn't give any names.
The developments point to the sensitivity of the Darfur conflict for the military that arrested al-Bashir after four months of deadly street demonstration against his 30-year rule. That it was not until this week, however, that the army turned against him.