Maharaj, who has played 36 Tests and 14 One Day Internationals (ODIs), is yet to make his T20I debut.
In the 104 T20s, the left-arm spinner has 83 wickets at a strike rate of 26 and an economy of 6.62.
Bjorn Fortuin and Tabraiz Shamsi are the other two spinners while George Linde has been picked as one of the three reserve players. There was no room for veterans Francois du Plessis, Imran Tahir and Chris Morris.
All-rounder Wiaan Mulder, who has played four T20Is so far for South Africa, has also been named in the side which will be led by Temba Bavuma.
South Africa have been placed in Group 1 in the Super 12 stage with England, Australia, West Indies and two qualifiers. They will start their campaign against Australia in Abu Dhabi on October 23.
South Africa Squad: Temba Bavuma, Quinton de Kock, Bjorn Fortuin, Reeza Hendricks, Heinrich Klaasen, Keshav Maharaj, Aiden Markram, David Miller, WIaan Mulder, Lungi Ngidi, Anrich Nortje, Dwaine Pretorius, Kagiso Rabada, Tabraiz Shamsi and Rassie van der Dussen.