The Pretoria High Court is yet to rule on whether he should be handed over to the International Criminal Court (ICC) who have charged him with the crimes.
The Sudanese leader who is in Johannesburg for an African Union (AU) summit was seen leaving his hotel in a black BMW and reportedly heading to Waterkloof air force base in Pretoria.
Mr Bashir's plane at the Waterkloof air force base in Pretoria fuelled up late on Sunday night and its crew has obtained final clearance to take off and could leave at any time on Monday, says the BBC's Nomsa Maseko in Pretoria.
Government forces and allied Arab militias are accused of targeting black African civilians in the fight against the rebels.
Mr. al-Bashir is accused of committing war crimes, including crimes against humanity and genocide during the Darfur conflict. |
UN Secretary-General Ban Ki-moon had on Monday said the ICC's warrant for the arrest of Mr Bashir must be implemented by countries who have signed up to the court's statutes.
As a member of the ICC, South Africa is obliged to arrest anyone charged by the court. Before the summit, the ICC issued a press statement urging the South African government "to spare no effort in ensuring the execution of the arrest warrant".