The 30-year-old sustained the problem during the Proteas' tour of Australia in November and has not featured in the current Test series against the Windies.
South Africa had hoped to have the batsman back for the second Test in Port Elizabeth, but he was not fit enough to be involved.
However, he has been named in the T20 squad - but Cricket South Africa confirmed he will only be considered for the final game in Durban on January 14 to ensure he has fully recovered.
The hosts have rested a number of players - including Hashim Amla, AB de Villiers and Dale Steyn - for the three matches with the Cricket World Cup in mind, so Faf du Plessis will resume his role as captain.
Joining Duminy back in the squad is spinner Aaron Phangiso after he missed the tour of Australia through a finger injury, and wicketkeeper-batsman Morne van Wyk who replaces the injured Quinton de Kock.
Cape Town hosts the opening T20 on January 9, before the sides travel to Johannesburg and Durban.
A five-match one-day international series then follows.
South Africa squad in full:
Faf du Plessis (captain), Kyle Abbott, Farhaan Behardien, Marchant de Lange, JP Duminy, Reeza Hendricks, Imran Tahir, David Miller, Wayne Parnell, Aaron Phangiso, Kagiso Rabada, Rilee Rossouw, Morne van Wyk, David Wiese