The International Criminal Court (ICC) said it was "disappointed" at South Africa's failure to heed its calls to detain Bashir on long-standing arrest warrants over the Darfur conflict.
As his plane took off on the final day of an African Union leaders' summit in Johannesburg, the local high court was still hearing arguments over an urgent application to force the authorities to detain him.
"Our position has always been that South Africa's obligation is clear and unequivocal. It had an obligation to arrest him," the ICC's chief deputy prosecutor James Stewart told AFP.
"The conduct of the respondents -- to the extent that they have failed to take steps to arrest and detain (Bashir) -- is inconsistent with the constitution of the Republic of South Africa," Mlambo said.
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President Bashir's hurried departure from Waterkloof military airport outside Pretoria sparked anger from rights groups.
"When he took off from South Africa today, he took with him the hopes of thousands of victims of grave crimes in Darfur who wish at last to see justice done," Human Rights Watch said in a statement.
South Africa is a signatory of the ICC, which has often been criticised for only targeting African leaders.
Dressed in his traditional white robes, Bashir waved his cane in the air as he stepped off the plane in Khartoum.
He then drove around outside the airport in an open-topped car amid a crowd of around 1,000 supporters.
Bashir's "participation (at the summit) confirms the president is one of Africa's leaders," Sudan's Foreign Minister Ibrahim Ghandour told a new conference.