Philander took three for 26 in a Pakistan total of 179 all out.
Captain Misbah-ul-Haq top-scored for his team with 79 not out but no other batsman reached 30
Philander, recently recalled to the one-day side after starring for the South African Test team, struck with the fourth ball of the match when Ahmed Shehzad was caught at first slip without scoring.
Shehzad made a century when Pakistan clinched the series by winning the second match in Port Elizabeth on Wednesday.
With the series decided, both sides showed several changes.
Jacques Kallis and Dale Steyn, both with minor injuries, were rested from the South African team, while Graeme Smith was absent because of a family bereavement.
Pakistan made four changes. Mohammad Hafeez and Junaid Khan were injured, according to captain Misbah-ul-Haq, while Shahid Afridi and Nasir Jamshed were rested. The new players were Umar Amin, Asad Shafiq, Sohail Tanvir and Abdur Rehman.
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