Shahid Afridi (3-28) was the pick of the bowlers as the Proteas were restricted to 4-170 at Newlands in reply to Pakistan's 4-176, with JP Duminy's quickfire 47 not out and 48 from Hashim Amla proving to be in vain.
Umar Akmal equalled his record score of 64 in the shortest format of the game and skipper Mohammad Hafeez made 63 in a total that proved to be enough to deny South Africa another series victory.
South Africa had won the first game of the series on the Duckworth-Lewis method, having also won both games in the two-match T20 series in Dubai earlier this month and the last three games of the one-day international series in the Middle East.
After winning the toss and electing to bat, Pakistan lost Ahmed Shehzad (9) when he edged Wayne Parnell's first ball to Amla at slip.
Aaron Phangiso struck with his second ball of the eighth over as Nasir Jamshed (16) was stumped by Quinton de Kock, but Hafeez and Akmal then combined for a third-wicket partnership of 102 with Phangiso (1-33), Morne Morkel (0-37) and Parnell (1-37) proving to be expensive.
Dale Steyn (2-29) then had Hafeez caught at mid-off by AB de Villiers and the paceman stuck again when Duminy took a fine catch to end Akmal's impressive knock, but Pakistan posted a competitive total.
In South Africa's reply, Amla and De Kock (28) put on 58 for the first wicket before Afridi took a wicket with his first ball when Jamshed caught the the wicketkeeper at deep fine leg.
The experienced Afridi then saw the back of Faf du Plessis (six) and the dangerous De Villiers (13) to reduce the home side to 3-87 in the 12th over.
Duminy showed his intent by smashing Afridi down the ground for the first of his two sixes, but Amla was caught by Bilawal Bhatti off Saeed Ajmal (1-30) with South Africa still needing 60 to win off just 27 balls.
Left-hander Duminy made a good fist of it with his 47 coming from just 26 balls and he put on an unbroken partnership of 53 with David Miller (22 from 13), but Pakistan were not to be denied.