At tea Younus was 29 not out in Pakistan's second innings off 56 for three after he was dropped by Jacques Kallis in the final over before the interval.
Pakistan, who lead 1-0 in the two-Test series, still trailed the world number one side by 362 runs after they were dismissed for 99 in their first innings.
Earlier, South Africa added 57 runs to their overnight total of 460 for four with captain Graeme Smith (234) and AB de Villiers (164) falling to Saeed Ajmal and Mohammad Irfan respectively.
Irfan was suspended from bowling for the remainder of the innings after he was given a third warning by the umpires for running on the pitch.
When Pakistan batted again, Dale Steyn and Vernon Philander took a wicket each in the first two overs of the innings.
Openers Shan Masood and Khurram Manzoor both failed to score and Azhar Ali fell after lunch lbw to the first ball from occasional off-spinner JP Duminy for 19.