Gen Bashir proclaimed himself chairman of a 15-member Revolutionary Command Council (RCC).
He signed a "constitutional decree" dismissing the government and other state bodies.
Its charges against Mr al-Bashir stem from reported atrocities in the conflict in Sudan's Darfur region, in which 300,000 people were killed and two million displaced in the government's campaign, according to UN figures.
Raising his stick: Mr al-Bashir, who has been in office since a 1989 military coup, is wanted by the International Criminal Court on war crimes allegations linked to the conflict in Sudan's Darfur region South African officials have declined to comment, though government lawyer William Mokhari said African leaders at the summit in Johannesburg had immunity and there was no basis for arresting Mr al-Bashir.
The coup was also aimed at preventing the signing of a peace treaty with John Garang's Sudan People's Liberation Movement (SPLM).
General Bashir opposed the plan, which would have allowed secular law, instead of Sharia, in the south.
Lift off: A plane carrying Sudanese president Omar al-Bashir leaves Waterkloof Air Force Base in Pretoria, South Africa, today after he ignored a court order to stay in the country to face genocide charges Facing a fight: The ICC's charges against Mr al-Bashir stem from reported atrocities in the conflict in Darfur in which 300,000 people were killed and two million displaced in the government's campaign In a government notice published June 5, South Africa's minister of international affairs, Maite Nkoana-Mashabane, signed an agreement granting diplomatic immunity to delegates participating in the African Union summit.
Mr Kenyatta, who is attending the summit in Johannesburg, was charged in 2011 as an ‘indirect co-perpetrator’ in post-election violence that left more than 1,000 people dead in 20.
His other military posts included military attach in the United Arab Emirates (1975-79), garrison commander (1979-81) and head of the armoured parachute brigade in Khartoum (1981-87).
From 1989 to 1993 he was also Sudanese minister of defence.
National salvation On 30 June 1989 he led fellow officers in a mutiny against Prime Minister Sadiq al-Mahdi.
General Bashir said in a televised communique that the coup was "to save the country from rotten political parties".
The basins in the courtyard date from the periods of Fatih Sultan Mehmet (1451-81) and Sultan Murat III (1574-95).