In the end, it was decided Watson's calf strain was too much of a risk and he will be given more time to get himself right for the third test in Perth.
Australia stuck with the same side that secured a draw against the world No 1 Proteas at the Gabba, with Ben Hilfenhaus retained in the pace attack and young left-armer Mitchell Starc again missing out.
"Once we got here, our intent was to give Watto every chance, as a very important player and vice-captain of the team but, unfortunately, we've run out of time," Clarke said.
He said he and the selectors stuck with Hilfenhaus because they saw great improvement from the bowling attack in the latter days of the Brisbane test.
"I thought the bowlers came back really well. We took 14 South African wickets where they took five of ours," he said.
"I think we've got a good combination. We've got a good mixture of aggression but also bowlers who can bowl long spells and dry runs up if required out there on that wicket.
"Generally in Adelaide, you have to bowl quite tight during periods of the game."
- AAP
