According to a Cricket South Africa media statement, Rabada suffered from the injury during the three-match T20I series against Australia which the visitors won 2-1 on Wednesday evening.
Cricket South Africa Chief Medical Officer, Shuaib Manjra said: "Kagiso (Rabada) sustained a groin muscle strain in the T20 series against Australia, he was assessed by the medical staff, assisted by an MRI scan."
The injury puts Rabada out of action for four weeks which means that he should regain his fitness before the Indian Premier League (IPL) starts on March 29.
The three-match ODI series between South Africa and Australia ends on March 7, after which the Proteas will travel to India where they will play their first match on March 12 in Dharamsala.
Meanwhile, right-handed batsman Temba Bavuma has recovered from the hamstring issue that had kept him out of the Australia T20Is and will be available for the ODI leg of the tour which starts on Saturday in Paarl.