The 24-year-old will be out of action for four weeks after suffering the injury during the final T20 international against Australia on Wednesday.
South Africa after losing the T20 series 1-2, are now locked in a three-match ODI series with Australia.
“Kagiso sustained a groin muscle strain in the T20 series against Australia, he was assessed by the medical staff, assisted by an MRI scan,” Cricket South Africa (CSA), Chief Medical Officer, Shuaib Manjra said in a media statement.
“The significant injury means that he will take approximately four weeks to heal, which effectively rules him out of both the Australia and India ODI series,” he added.
The Proteas are scheduled to travel to India for a three-match ODI series, starting on March 12 in Dharamsala.
CSA also announced right-hand batsman Temba Bavuma has recovered from his hamstring injury and will be available for the ODI leg of the Australia tour.