The tourists responded superbly to their thumping 125-run defeat in the series opener at Bloemfontein, Mohammad Irfan taking four for 33 as the Proteas were all out for 191 in an encounter that was reduced to 44 overs per side due to heavy rain.
Despite a couple of scares early on in the chase, Misbah (57 not out) and Malik (35no) guided Pakistan to 192 for four before the 40th over with some assured batting.
Graeme Smith and Hashim Amla put on 22 in the opening four overs after South Africa had won the toss before the latter followed a wider one and edged Irfan behind for 17, while new man Colin Ingram also nicked to Kamran Akmal off the very next delivery.
AB De Villers became Irfan's next victim, with Younis Khan holding on in the slips.
Junaid Khan then got in on the act, Smith caught behind for 10 from a mistimed pull, while Faf du Plessis was sent back after a lively 17 when the giant Irfan got down well to pouch a caught-and-bowled chance to leave the Proteas reeling on 62 for five.
Farhaan Berhardien (58) and Ryan McLaren rescued the innings from meltdown, putting on 44 for the sixth wicket at an impressive rate.
McLaren eventually perished, the third man out for 17, when Mohammad Hafeez pinned him lbw.
Robin Peterson proved an even better foil for Berhardien, who passed 50 for the first time in internationals from 60 balls with a dashed two off Shahid Afridi.
Hafeez removed him just before the rain came with Peterson still in place on 39no.
A spectacular deluge raised questions over whether the game would even restart, but the ground's impressive drainage gave time for the innings to resume and meant only six overs per side were lost, although South Africa's tail end failed to shine on the resumption as they were all out for a below par score.
The tourists began their reply in a rather cautious fashion and an opening partnership of 29 was ended when Nasir Jamshed was caught at slip off McLaren.
Hafeez kept scoring at a decent rate but he was out for 31 after chipping Dale Steyn to midwicket, while Akmal departed in the next over when he was bowled by Peterson to leave Pakistan wobbling on 69 for three.
Captains past and present Younis and Misbah kept the score ticking over, although the pressure was starting to build before the latter thumped Kyle Abbott for six over long-off to end a nine-over boundary-drought.
Younis looked to be finding his gear but, two balls after sending Peterson through midwicket for four, he perished when he struck the same bowler's full toss to deep square-leg.
That brought together Misbah and Malik, who settled into his stride by taking four fours off a Lonwabo Tsotsobe over before despatching Peterson for a leg-side six.
The pair had taken Pakistan well ahead of the required run-rate and refused to take any risks, although Misbah hammered McLaren back over his head for his third four before bringing up his half-century with a single off the next ball.
South Africa's misery was compounded when, with Pakistan needing a single for victory, Abbott's third ball of the 40th over was called a wide.