With the series on the line against Australia, Rabada endured one of his more difficult days with 18 wicketless overs that went for 81 runs while he also had to leave the field three times.
It came as Australia reached 4-330 at stumps on day two in reply to the Proteas' first-innings 329, handing them the lead and control of the Test.
On the day he was announced as the world's No.1-ranked Test bowler, Marco Jansen also required some treatment on field for stiffness, as the Proteas' bowling fell away late in the day.
Rabada's situation comes after Australia had similar battles in Gqeberha last week, with Josh Hazlewood struck down by food poisoning as South Africa took the game away from them.
"He's got some stomach cramps," Proteas bowling coach Piet Botha said of Rabada.
"I think it's just something that came about today. He wasn't at his best today but hopefully he will recover soon."
Jansen removed Matt Renshaw (74) and Cameron Green (65) in back-to-back overs, but Botha said the 206cm quick was battling soreness.
"Marco just had a bit of stuff rubbed into his back during the break," said Botha.
"It's obviously a little bit of stiffness, I'm not too sure what it is. We'll check deeper into what is the problem, but I don't think it's serious.
"We're three weeks into the cricket, so you can expect guys are getting a little pain here and pain there through fitness and bowling a lot of overs."
Beyond Rabada and Jansen, Gerald Coetzee was largely ineffective after being the preferred man to replace the injured Anrich Nortje.Â
Botha said he would rate the Proteas' bowling as a "six-out-of-10" after Australia took a largely risk-free approach to batting and accumulated runs.
The Proteas bowlers were left to rue their batters' fall from 1-203 to all out for 329, wasting a good start and flat wicket over the opening days.
"We always knew it would be a tough day the way the wicket was playing. No lateral movement there," Botha said.
"It was always going to be about the effort, I can't fault that. There was effort there the whole day.
"Maybe if we're self-critical, we didn't hit our length for long periods of time.
"Because once the wicket plays like that you have to create some maidens and hopefully you get a false shot."
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