Bangladesh's all-time leading all-rounder was reappointed T20 captain after a seven-year gap following the retirement from the format of Mashrafe Mortaza.
He takes over a squad that has already suffered humiliating defeats in two Test matches and three One-day Internationals.
So poorly have Bangladesh performed that Test captain Mushfiqur Rahim and one-day skipper Mortaza were unable to hide their frustration in comments to Bangladesh media.
"I am not able to motivate my players or guide my bowlers," Rahim was quoted as saying after the Tests.
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While Bangladesh's batsmen were always expected to struggle in South African conditions, the bowlers have been the most conspicuous failures on the tour.
In two Tests and three one-day internationals, the bowlers have captured only 23 wickets at a combined average of 100.21.
With no new faces in the T20 squad and leading bowler Mustafizur Rahman having returned home because of injury, Shakib appears to have the odds stacked against him.
South Africa, though, will be without inspirational captain Faf du Plessis, who suffered a lower back disc injury in the final one-day international, which will keep him out of action for six weeks.
The hosts have rested two of their leading bowlers, Kagiso Rabada and Imran Tahir.
The South Africans lost a T20 series against Sri Lanka last season despite outclassing them in the Tests and one-day games.
With South Africa fielding an unusually inexperienced bowling line-up, Bangladesh's batsmen will hope to seize the opportunity to make a strong finish to the tour.
South Africa's batting looks formidable, however, and the Bangladesh bowlers will need to perform far better than they have in previous matches if they are to contain them.
South Africa: JP Duminy (capt), Hashim Amla, Farhaan Behardien, Quinton de Kock (wkt), AB de Villiers, Robbie Frylinck, Beuran Hendricks, David Miller, Mangaliso Mosehle (wkt), Dane Paterson, Aaron Phangiso, Andile Phehlukwayo, Dwaine Pretorius, Tabraiz Shamsi.
Bangladesh: Shakib Al Hasan (capt), Imrul Kayes, Liton Das (wkt), Mahmudullah, Mehidy Hasan, Mohammad Saifuddin, Mominul Haque, Mushfiqur Rahim (wkt), Nasir Hossain, Rubel Hossain, Sabbir Rahman, Shafiul Islam, Soumya Sarkar, Taskin Ahmed.