"Yes, he has left," minister Ahmed Bilal Osman confirmed, saying that South Africa had always agreed not to arrest the president while he was in the country for the African Union summit.
The South African state broadcaster, SABC, first reported at about 10:15 GMT on Monday that President Bashir's plane had flown out of the Waterkloof air force base, on the outskirts of Pretoria.
The lawyer appearing on behalf of the South African government, however, told the high court in Pretoria that President Bashir was not on the list of passengers in the Sudanese plane that left Waterkloof base.
Earlier, Sudanese Information Minister Osman told Al Jazeera the president would return to Sudan on Monday.
"He is coming back to our country in one or two hours," Osman said, adding that it did not matter if the court ordered Bashir's arrest, as it had no ability to enforce such an order.
"The judiciary...does not have policemen. The president is there (in South Africa) and no one is going to arrest him."
An interim order was made by the high court in Pretoria on Sunday, barring President Bashir from leaving the country pending an application from civil society organisations, calling for his arrest.
The state lawyers were expected to start their arguments at 08:00 GMT before the court in Pretoria on Monday, sources told Al Jazeera. The high court has to decide whether to send Bashir to the International Criminal Court.
Al Jazeera's Fahmida Miller, reporting from Johannesburg, said that the Sudanese president's plane had been moved to a South African military base late on Sunday night.
Bashir, who is accused of war crimes in repressing an armed uprising in the Sudanese region of Darfur, was due to appear in Johannesburg on Sunday for the AU summit.