Pakistan, set a target of 354 runs after South Africa declared their second innings at 203/5, had reached 153/3 on final day of the second Test.
South Africa captain Graeme Smith faces a race against time to get fit for next month's first Test against India after an x-ray revealed an undisplayed fracture.
Pakistan left-arm spinner Abdul Rehman took three wickets and scored his maiden half-century to foil South Africa's attempts to win the second Test.
Skipper Misbah-ul-Haq and Azhar Ali led Pakistan's fightback with fifties apiece to keep South African hopes of enforcing follow-on at bay in the 2nd Test.
AB de Villiers became the highest scorer in a Test innings for South Africa when he made 278 not out against Pakistan on Day 2 of the second Test.
AB de Villiers and Jacques Kallis rescued South Africa with hundreds to guide them to 311/5 at close on the first day of the second Test against Pakistan.
Pakistan captain Misbah-ul-Haq won the toss and put South Africa into bat in the second and final Test at Abu Dhabi Stadium on Saturday.
SA captain Graeme Smith said he would like to end the tour with a clean sweep in all three formats of the game as they take on Pakistan in the second Test.
Rival captains Misbah-ul-Haq and Graeme Smith hailed Younis Khan's brilliant hundred which helped Pakistan salvage a fighting draw in the first Test on Tuesday.
Younis Khan scored unbeaten 131 as Pakistan reached 343 for 3 on the fifth and final day of the first Test match against South Africa on Tuesday.