New Zealand had won with a penalty goal in the last few moments, just as South Africa won a Test against the British & Irish Lions with a penalty goal, and Australia had managed the same against them.
"I thought the game plan worked," he said.
"I thought we had opportunities, I thought they had opportunities. It probably came down to the wire – a call here, a bounce of the ball there…Sometimes it goes for you, sometimes it goes against you. So, I think it's swings and roundabouts," he said.
Nienaber said it felt it had been a proper Test match with small margins reflecting the respective DNA of the two sides' styles.
"Rugby would be incredibly boring if everyone played the same tactics and we might not do the same tactics next week like they might not do the same tactics," he said.
The Springboks believed they had it in them to beat the All Blacks, and they knew it would come down to a narrow margin as that had been the case in contests between the side in recent years.
However, he defended the Springboks style of play the Springboks used, a style criticised for being one-dimensional by some and boring by others.
"We always want to attack space, and I back the players to make good decisions," he said.
"If we can create a one-on-one with a passing game, or through the kick, then it's basically the same thing. So, we do try to identify where that space may be, and look to create those one-on-one situations," he said.
Nienaber said they continued to concede too many offside penalties, and their discipline would need to be looked at.
"But, overall, I think there was a big step up in this game, and we were a lot more on song in terms of our preparation," he said.
Captain Siya Kolisi said the tactical approach was about doing what they knew best and doing it properly.
"It was really intense, and heated, a real proper game of rugby with speed and intensity. I can't say where it went wrong, but I thought our plan was the correct one," he said.
Kolisi said even in the desperate last moments of the game as they attempted to secure their win, there was no need to change from their kicking strategy.
The message among the players was to stick to the game plan.
"That's how we know how to play, and it's always worked for us. We were never going to change anything because that's how we won the game ball back. So, I really like that because it's been working the whole day, so why change at the end?" he said.