Springbok and hard man hooker Malcolm Marx said it was a tough contest, especially up front where the All Blacks had managed to upset the South Africans.
While he and loosehead prop Steven Kitshoff struggled to isolate one key thing in the All Blacks approach they did feel the All Blacks had found ways to disrupt the Springbok scrum.
Marx said: "There were one or two calls that went our way and one or two that didn't. The All Blacks have a quality set-piece.
"It was always going to be tough to execute our plan against them. It was really tough," he said.
The All Blacks had kept South Africa guessing at scrum time.
"We didn't see a consistent picture and everything changed at each scrum. We just have to assess and adapt to the situation much quicker," he said.
Kitshoff said the Springboks needed to be able to think on their feet and to develop the ability to find real time solutions.
"They disrupted what we planned. We need to fix it on the field. You have to find solutions while we are playing. You can't say afterwards that this and that went wrong," he said.
That was easier said than done, Marx said.
"Everything happens so quickly, you easily see what goes wrong," he said.
The lineouts proved a different case and the Springboks had been able to secure their ball. However, their lineout maul was given no chance to get going.
"We couldn't get our maul going because of their sacking. That worked pretty well for them.
"We can't cry over spilt milk. This result didn't go our way so now we start prepping for next week's game," he said.
Kitshoff said the ruck had also been a source of frustration for his side.
"Sometimes you felt you have the ball and it doesn't go your way. It was a real physical confrontation," he said.
South Africa meet Namibia on Saturday while the All Blacks play Canada on Wednesday next week.