Bashir had travelled to Johannesburg for an African Union summit that was overshadowed by the International Criminal Court (ICC) calling for him to be detained on long-standing arrest warrants over the Darfur conflict.
Even as his plane took off from Waterkloof military airport outside Pretoria, the local high court heard legal arguments over the application to force the authorities to arrest him.
Yesterday, Judge Hans Fabricius ordered authorities to stop Bashir from leaving the country after the Southern African Litigation Centre, a legal rights group, lodged its urgent case.
"(The) world stood (with) South Africa to fight apartheid but it stands for impunity for mass murder of Africans," Kenneth Roth, director of Human Rights Watch, said on Twitter.
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"South Africa has shamefully flouted ICC and domestic court to free man wanted for mass murder of Africans," he added.
South Africa is a signatory of the ICC, which has often been criticised for only targeting Africa leaders.
"President Bashir's plane took off from Johannesburg and will arrive around 6:30 pm (local time)," State Minister for Information Yasir Yousef told AFP in Khartoum.
At the summit, Bashir attended a group photograph yesterday along with South African host President Jacob Zuma and Zimbabwe's President Robert Mugabe, who is the chair of the 54-member group.
Today is the closing day of the summit.
Sudan officials in Johannesburg had earlier brushed off the court case and said the South African government had given them assurances about Bashir's trip before the summit.
The ICC indictments relate to the western Sudanese region of Darfur, which erupted into conflict in 2003 when black insurgents launched a campaign against Bashir's Arab-dominated government, complaining of marginalisation.
The United Nations says 300,000 people have been killed in the conflict and another 2.5 million forced to flee their homes.