Dlamini-Zuma – The first woman elected to head the commission – beat Jean Ping of Gabon in a close election on Sunday at a summit.
"My election should not be seen as a personal victory but it should be seen as a victory for the African continent in general," she told reporters before flying back to South Africa.
"We [will] continue to work in a way that tries to build consensus," added Dlamini-Zuma, who earlier posed for pictures with Ping.
Many participants in the AU summit, which ran over into the early hours of Tuesday, appeared relieved that the six-month impasse over the continental body's top job had finally been broken.
"One man in his time plays many parts, I have played my part and I now take my bow," Ping said at the closing ceremony.
One Western diplomat noted "a definite sense of relief" within the AU after the vote.
But the "very tough and aggressive" campaign waged by the candidates "will leave scars and resentment" he said, asking not to be named, particularly "if the South Africans did indeed bring pressure to bear," as some leaders have alleged.
Presidency spokesperson, Mac Maharaj, said he hoped the new appointment would result in a "more effective" AU.
"The African Union has taken many very good decisions. The problem is to get them implemented," he told journalists.
Zuma's office said he was "humbled by the confidence that Africa has showed in the Southern Africa candidate".
Reaction from the rest of the continent was mixed.
Sudan, whose conflict with South Sudan has been a key issue at the two-day summit, said it respected the choice of Dlamini-Zuma.
"We accept … and we respect the opinion of the leaders," said Rabbie Abdelatti Ebaid, a senior member of Sudan's ruling National Congress Party.
Breaking the deadlock
Kenya, which voted for Ping, conceded that the breaking of the deadlock was good for the continent, with Richard Onyonka, an assistant foreign affairs minister, calling the vote "a kind of victory for Africa because we have moved forward."
But he said he disapproved of South Africa's tactics that caused divisions within the AU.
"I'm very uncomfortable with the methods and style of South Africa. They were entitled to bring a candidate … but we felt that there was too much intimidation, arm-twisting and threats."
Another delegate, who did not want to be identified, accused South Africa, home to the continent's largest economy, of buying votes.
Dlamini-Zuma (63) is a veteran of the fight against apartheid. A doctor by training, she has also served as health and foreign minister.
Voting took place at the AU summit where leaders also focused on the continent's flashpoints, including Mali, the crisis between Sudan and South Sudan and escalating violence in eastern Democratic Republic of Congo.
On Sunday, Kigali and Kinshasa agreed to an international force to neutralise rebels in eastern DRC, as the AU said it was ready to send peacekeepers.
Rwandan President Paul Kagame said both sides had agreed "in principle" to accept the force.
He was speaking after his first face-to-face meeting with his DRC counterpart President Joseph Kabila since a UN report in June accused Rwanda of supporting Congolese rebels.
Dlamini-Zuma's win follows her challenge six months ago to unseat Ping, which ended in deadlock after neither won the required two-thirds of the vote, leaving Ping in the post.
Officials said the election this time went to four rounds of voting before Dlamini-Zuma won 37 votes, three more than the required majority.
The vote raised tensions between Africa's French and English-speaking countries. South Africa also drew accusations of violating an unwritten rule that the AU top job should go to a candidate from one of the continent's smaller countries.
While neither her camp nor the presidency has said whether or not Dlamini-Zuma will continue in her Cabinet post as home affairs minister, it is believed she will not be able to fulfil the two roles adequately.
"It is the prerogative of the president [Jacob Zuma] to decide if the minister will continue in home affairs. We will take our lead from there," Ronnie Mamoepa, Dlamini-Zuma's spokesperson told the Mail & Guardian on Monday.
The ANC said it would be difficult for Dlamini-Zuma to continue in her current portfolio as home affairs minister.
"As far as we're concerned it's a full-time position at the AU Commission, but it's a government decision so we won't comment on the minister's future," party spokesperson Keith Khoza told the M&G.
Dlamini-Zuma has brought tangible changes to home affairs, previously regarded as a hotbed of corruption and incompetence, a place staffed with government officials who took bribes and slept on the job.
A technocrat at heart, Dlamini-Zuma took over the department in 2009.
Dlamini-Zuma's appointment has left some parties and analysts jittery about the vacuum she leaves behind.
"We think it's great that Dlamini-Zuma was elected to the AU," Democratic Alliance spokesperson Mmusi Maimane told the M&G. "But there are concerns as to who her successor will be. Home affairs have delivered incredible results and it will be a tough job to find a suitable individual.
"Hopefully it won't be another crony of President Jacob Zuma; we need to the right person to continue her legacy," Maimane added.
But Professor Steven Friedman, director at the University of Johannesburg's Centre for the Study of Democracy, believes it won't be hard to find a replacement.
"Dlamini-Zuma did help to put home affairs on a more productive course, but there is no reason to believe her successor won't carry on in the same vein, ministers don't work alone at the end of the day," said Friedman.
He said the best way forward would be to have a replacement that provides continuity in the department.
"Her replacement must be capable of continuing with her mandate and should send a clear message that there will be no change. If not, there may be problems." – Sapa-AFP, staff reporter