Watson tweaked his calf while training in Potchefstroom last week, and on Saturday night (AEDT) was officially ruled out of the opening clash of the three-Test series when he was unable to run at full pace in Johannesburg.
Australia physio Alex Kountouris suggested it was a low-grade muscle injury, something they initially expected would not prevent Watson from taking the field on Wednesday in Centurion.
"We need a few more days now to let him recover and start up again," Kountouris said.
"Even as a batsman (he could not have played)."
Alex Doolan will now almost certainly debut at first drop, while Watson's timeframe for return is uncertain.
"I think he's a good chance to play (in the second Test), but we need to see what he gets from this (setback)," Kountouris said.
"Hopefully he gets to the point where he's able to train unrestricted by two or three days' out (from the Test), which is what we were planning to do here."
The squad has only three days off between day five of the first Test in Centurion and the start of the second match in Port Elizabeth, and Kountouris admitted Watson's recovery would be unpredictable.
"He's had these before ... they can take a short period of time or they can take an extended period of time. In this case it's looking like it's going to be a little bit longer," he said.
"You've just to got to go gradually. If he feels it you've got to stop again. Trying to manage it is a balancing act.
"Our first priority is to try and get him back as a batter, give the selectors that option (of playing him as a batsman)."
Earlier this week both coach Darren Lehmann and team doctor Peter Brukner insisted Watson would bowl before the first Test and be fine to play.
"We just managed it and he wasn't too bad," Kountouris said of the squad's initial optimism.
"We thought 'He's had this before, let's just nurse it'."
The 32-year-old played all 10 matches in the back-to-back Ashes series, overcoming hamstring and groin niggles to take part in the Brisbane and Sydney Tests respectively.
Kountouris noted Watson was very disappointed to be missing his first Test since returning home from India amidst 'homework-gate'.
"As we all are. We were very happy we got everyone through the past Ashes," he said.