The short answer is simple. It’s cricket. It’s inherently uncertain. And it doesn’t take a lot to go wrong to lose a Test match against good opposition. And South Africa are very good opposition, whatever the conventional wisdom about about how the current side falls short relative to the one which had olympian figures like Graeme Smith and Shaun Pollock.
Basically, Marco Jansen got 12 wickets in 69 false shots and Simon Harmer got 17 in 92 – a convenrsion rate neither bowler has achieved in his career before this series (and is not likely to again). For IND, the 5 regular mainstays of the IND batting after the Kohli-Pujara-Rahane-Rohit era – Yashasvi Jaiswal, KL Rahul, Shubman Gill, Rishabh Pant and Ravindra Jadeja – scored 2 fifties between them in 18 innings in the series. They survived 7 false shots per dismissal and made 309 runs at 18.2 runs per dismissal in the series. In England a few months ago, the same five batters averaged 65.7 runs per dismissal and made 2692 runs in the Test series. In England, they survived 15 false shots per dismissal. Against South Africa these batters played a false shot every 5.4 balls, to one every 7.1 balls in England.
Finally, the two Indian captains both lost the toss.
Put these three facts together, and its not difficult to see why South Africa won a close first Test in which India played 10 v 11, and a one-sided second Test in which South Africa won the toss and ran away with the match. Test matches are almost always decided because things go wrong for one team more than they do for another. They are not decided because one team makes bad decisions and the opposition doesn’t.
The details of the cricket are interesting (they usually are). For instance, both Harmer and Jansen have extraordinarily high release points. Harmer has a lot more experience than Washington Sundar. Harmer is 36, while Washington Sundar is only 26.
For a longer discussion about those, see this. But when you listen to it, keep in mind that the record presented here only explains why the probabilities nudged towards South Africa. They do not guarantee a 2-0 SA win. That outcome is down to luck.