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The Proteas are without their frontline paceman Dale Steyn, who has returned home for a rest, and Hashim Amla, who has also returned home for the birth of his child.
Steyn will return for the third one-day match in Abu Dhabi on November 6.
Robin Peterson is suffering from a viral illness and was not considered for selection.
South Africa included leg-spinner Imran Tahir who took eight wickets in the second Test in Dubai, which the Proteas won to square the two-match series 1-1.
Pakistan included three pacemen in Mohammad Irfan, Wahab Riaz and Sohail Tanveer.
The remaining one-day matches will be played in Dubai (November 1), Abu Dhabi (November 8) and Sharjah (November 11).
Teams:
South
Africa:
Colin Ingram, Graeme Smith, JP Duminy, AB de Villiers (captain), Faf du Plessis, David Miller, Ryan McLaren, Wayne Parnell, Morne Morkel, Imran Tahir, Lonwabo Tsotsobe.
Pakistan:
Ahmed Shehzad, Nasir Jamshed, Mohammad Hafeez, Misbah-ul-Haq (captain), Umar Amin, Umar Akmal?, Shahid Afridi, Sohail Tanvir, Wahab Riaz, Saeed Ajmal, Mohammad Irfan
Umpires: Richard Illingworth (ENG) and Shozab Raza (PAK)
TV umpire: Steve Davis (AUS)
ICC match referee: Ranjan Madugalle (SRI)