Smith has been allowed time off following the death of his grandmother, Cricket South Africa said on Friday.
South Africa are also without fellow stalwarts Jacques Kallis and Dale Steyn, who are sitting out the game as a precaution because of the three-match 50-over series against India starting next Thursday which will be followed by two tests.
Paceman Steyn has a mild side strain while all-rounder Kallis has a badly sprained little finger.
Pakistan have already won the series against South Africa after success in the first two ODIs in Cape Town last Sunday and Port Elizabeth on Wednesday.
(Reporting by Mark Gleeson; Editing by Alison Wildey)
- Sports & Recreation
- Graeme Smith
- South Africa
- Jacques Kallis
- Cricket South Africa
- Dale Steyn