Put into bat in a rain-hit encounter, Pakistan rode on Misbah-ul-Haq's 56 to post 222 all out in 46.4 overs and then packed South Africa for 202 in 33.3 overs in the 47 overs-a-side game.
Chasing a revised 232-run target, Proteas innings fell apart in the face of some excellent Pakistan bowling as captain AB de Villiers' valiant 77 went in vain on a lively Eden park track.
South Africa were in neck deep trouble at 138 for seven, before de Villiers stuck to his guns, forming crucial partnerships with Dale Steyn (16), Kyle Abbott (12) and Morne Morkel (6 not out) for the seventh, eight and ninth wickets respectively.
But it was Pakistan's day after Irfan, Rahat and Riaz ran through the South African top-order of Quinton de Kock (0), Hashim Amla (38) and Faf du Plessis (27) to put the African giants in early trouble.
Earlier, Pakistan showed some application when they batted after wicketkeeper-batsman Sarfaraz Ahmed, who took five catches behind the stumps, gave the team a good start with a gritty 49.
Younis Khan (37) and Shahid Afridi (22) also chipped in with crucial scores apart from Misbah's patient half-century that did the trick for the Men in Green.
Dale Steyn, who bagged three wickets in the Pakistan innings, was also responsible for opener Ahmed Shehzad's (18) scalp with a breathtaking catch in the outfield.