Saturday's win was an improvement on the Welsh series in July, he said.
"I think we have built on stuff that we thought there was good growth in the Wales series. I think we are slowly building our game, but I don't think it is the finished product yet."
Nienaber praised hooker Malcolm Marx's effort in his 50th Test.
"I thought he was outstanding – and that's Malcolm. He is the guy that exemplifies what a Springbok should be. He is a warrior, a guy who had to work hard to get where he is.
"He made the change from loose forward to hooker – so he really had to work hard to get where he is.
"I have worked with him since he was an Under-20 in 2014, and it is phenomenal to see what a guy he has become."
Captain and flanker Siya Kolisi said, "It feels good tonight, but we know the Championship is not done yet. We have five more games to go, but the next important one is next week [at Ellis Park].
"We set goals after the series against Wales of winning back-to-back series against the All Blacks and also addressing our record against the Wallabies overseas.
"There is plenty of work ahead of us in the Rugby Championship, But we are very pleased to have won in front of a fantastic crowd at Mbombela.
"I don't know how the people of South Africa do it with their incredible support for us with everything that is going on in our country.
"The atmosphere was unbelievable and, as players, we are reminded that it is never about us, and the odd mistake we make here and there, or the good things we might do as individuals. It is all about the people who come out, and how we, overall as a team, can pay them back."