He isn't injured, but he hadn't been selected into any test matches by team management after WTC also he expressed the frustration about not being selected for the test series which points that probably team management is intentionally avoiding him and there are many experts reported that this could be the end of his career.
He is one of the few players all around the world who only play in Test matches and he isn't great in the last couple of years but he always put a break if wicket falls initially and that is what really needed to be the test player, just consume 50 balls and score only 1 run still nobody cares while the evolution of cricket demand fast and stylish players so we winded up for 131 in the last inning.
I don't see any reason for not selecting Pujara into the test team. He and Rahane are the only batters who can stand against the pace and unsettled bounce of the South African bowlers. Both are of 35 years of age and are fit to play test cricket. I was reading an article on one of the prominent media house website and found that the selectors are looking for new beginning. If the selectors are trying to find a new player then they have failed miserably.