Set 451 for victory after the visitors declared their second innings on 318 for two, Younus stroked an unbeaten 131 as Pakistan lost just one wicket on the fifth day to reach 343 for three.
Younus got solid support from skipper Misbah-ul-Haq (76) as the pair put on an unbroken fourth-wicket stand of 186.
Their partnership was a record for any Pakistan wicket against South Africa, eclipsing the 161-run second-wicket stand between Kamran Akmal and Younus scored in Lahore [ Images ] during the 2007-08 season.
South Africa began the day with high hopes of pushing for victory but did not help their chances by spilling three catches.
Younus was dropped twice, with his score on 16 and 70, while Misbah was put down at short leg when he had scored just eight.
Pakistan began the day on 109 for two with Azad Ali and Younus at the crease.
The duo stretched their third-wicket stand to 82 before Ali, on 63, fell when he was bowled by left-arm spinner Paul Harris with a ball that beat the batsman's defensive prod to peg back his off stump.
The two teams will now turn their attention to the second, and final, match of the series which starts in Abu Dhabi on Saturday.