Philander, largely overlooked for the one-day side despite his success in Test matches, bowled with excellent control to record figures of three for 26 in his 10 overs and help to restrict Pakistan to 179 all out after the visitors were sent into bat having lost the toss.
South Africa never looked unduly troubled in their chase, reaching 181 for six with 68 balls to spare, captain AB de Villiers steering them home with a composed 48 not out.
Pakistan had already won the three-match contest heading into the final encounter, their first victory over South Africa in a bilateral limited-overs series.
Philander has taken 95 wickets in 18 test matches and emerged as one of the world's top bowlers in the longer format of the game since making his debut two years ago but this was just his 11th one-day appearance six years on from his first in 2007.
He set the tone early in the game, picking up the centurion from the last game, Ahmed Shehzad, for a duck in the first over of the innings.
He was the pick of a South African attack in which all the bowlers picked up wickets, Lonwabo Tsotsobe returning two for 38 in his 10 overs and Ryan McLaren two for 28 in eight.
Pakistan's Misbah-ul-Haq ran out of partners to be left stranded on 79 not out as the visitors were bowled out in the 47th over.
Hashim Amla (41) helped South Africa to get off to a fast start and although they lost wickets at regular intervals, they easily passed Pakistan's mediocre total on a good batting wicket.
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