Mr Mbeki said he was ready to meet Mr Bashir to discuss the implications
South Africa's president has called on the International Criminal Court not to prosecute Sudan's leader for war crimes in case it upsets Darfur's peace talks.
Thabo Mbeki told South African TV that Omar al-Bashir's continued presence as head of state was also needed to assist the country's post-civil war security.
The ICC's chief prosecutor sought an arrest warrant for Mr Bashir last week for alleged war crimes in Darfur.
On Wednesday, the Sudanese leader said he was not worried by the accusations.
"We're here to send a message to the world, we're people of peace, we want peace, we're the ones who make peace," said Mr Bashir.
Sudan's government has said it does not recognise the ICC or its decisions, and warned that any indictment could cause mayhem.
A three-judge panel at the ICC is currently considering whether there are reasonable grounds for any charges to be laid.
In an interview with SABC-TV on Friday, President Mbeki said it was important that both the peace process in Darfur and the rebuilding of post-civil war Sudan were not disrupted by the ICC decision.
ACCUSATIONS AGAINST BASHIR
Killing members of the Fur, Masalit and Zaghawa ethnic groups
Causing these groups serious bodily or mental harm
Inflicting conditions of life calculated to bring about these groups' physical destruction
Crimes against humanity:
Attacks on civilians in Darfur
Pillaging towns and villages
"Both of them require the very active participation of President Bashir," he said.
"I don't know how they would do that if an International Criminal Court says here's a person who has been indicted, because they then must stop interacting with him because this is a wanted criminal, and I don't know how you then implement all of those things," he added.
Mr Mbeki, who has been criticised for being soft on Zimbabwean President Robert Mugabe, said he was ready to meet Mr Bashir to discuss the implications.
The African Union has called for the UN Security Council to suspend the accusations, while the Arab League has warned they set a dangerous precedent.
ICC Chief Prosecutor Luis Moreno-Ocampo told judges at The Hague on 14 July that there were "reasonable grounds" for believing Mr Bashir bore criminal responsibility on 10 counts of genocide, crimes against humanity and war crimes in Darfur.
Some 300,000 people have died as a result of the conflict since 2003 while more than two million have fled their homes, the UN estimates.
Sudan's government denies mobilising Arab Janjaweed militias to attack black African civilians in Darfur after rebels took up arms.