The presidency will respond to Nkosazana Dlamini-Zuma's election as AU commission chairman after voting results are officially announced on Monday.
"The AU is yet to formally announce it. Until then it will be inappropriate to respond," spokesman Mac Maharaj said by phone from Addis Ababa, Ethiopia.
According to reports Dlamini-Zuma, who is home affairs minister, had received the most votes, beating the incumbent, Jean Ping of Gabon.
Earlier, International Affairs and Co-operation Minister Maite Nkoana-Mashabane said Dlamini-Zuma would make sure the African Union's resolutions were implemented.
"What should change [with her election]... is that there will be more accountability, there will be more fast-tracking of implementations of decisions taken by the heads of state," Nkoana-Mashabane told SAfm.
"That means, spend more time on implementation of our resolutions instead of just creating more and more [resolutions]."
Nkoana-Mashabane said Dlamini-Zuma's election on Sunday evening was a victory for women.
Dlamini-Zuma would through the AU "strengthen early warning systems, strengthen democracy and rule of law, and unity", Nkoana-Mashabane said.
The commission is the secretariat of the union entrusted with executive functions.
On its website the AU explains the commission plays a central role in the AU's day-to-day management. It represents the AU and defends its interests, elaborates the union's draft positions, and prepares and co-ordinates its strategic plans.