Mr Al-Bashir’s departure came hours before the Pretoria High Court will rule on whether he should be handed over to the International Criminal Court (ICC), who have charged him with war crimes and genocide.
The Sudanese leader was in Johannesburg for the 25th Assembly of Heads of State and government of the African Union.
On Sunday, the court ordered Mr Al-Bashir not to leave the country until the case had been heard.
Al-Bashir is accused of committing war crimes, crimes against humanity and genocide during the Darfur Conflict.
The UN says about 300,000 people in Sudan have died and more than two million have fled their homes since fighting began in 2003.
Government forces and allied Arab militias are accused of targeting black African civilians in the fight against the rebels.