ABs' game plan for the last few years has simply been to tackle until a counterattack opportunity presents itself. At that time, opposing teams don't have the personnel in line to defend, and a few slick passes later they're in (pricks).
The issue against the Boks: kicking the ball doesn't present the same opportunities. First you have to catch it under pressure, then you need to attack the space. And there isn't any on a planned kick-chase; ABs have a man in the air contesting against 1 Bok player, then 3-5 around for screening or support. Boks can throw in a couple of blokes to protect the ball if they get it back, then kick it again!
On attack, the ABs just spaced out wide and let the Boks number up. No subtlety, no short kicks, no changes of angle in their attack, or that drop-back pass we see from midfield to a sweeping playmaker to cause confusion and open up the line.
As a result, their support play at ruck time was rubbish because the Boks had Kwagga Smith and threw in enough numbers to slow it down if he wasn't winning it.
Throw in a few combination changes from the AB coaching staff vs a fairly settled Bok lineup, trying conditions unsuited for long phase play, and a Bok team that wanted rest breaks every 5 minutes, and you're going to get a mess.
Additionally: TJ Peranara isn't an international quality scrum half. He's just been allowed to hide his flaws in winning AB teams and become a complete smart arse about it. That pass at Havili's head... fuck a duck...