Pakistan trailed South Africa by one run after reaching 103 for two wickets at stumps on Saturday in its second innings on the third day of the first Test.
Opener Imran Farhat hit an undefeated 41 and Younis Khan was not out 32.
South Africa was dismissed for 417 before tea to take a 104-run first innings lead after the visitors were dismissed for 313 in their first innings at Centurion Park.
"We want to restrict Pakistan to a lead of less than 200 runs," South Africa batsman Ashwell Prince said. "If we can do that, I'm sure the guys will be confident of chasing down a target."
Jacques Kallis struck in his first over for South Africa, drawing Mohammad Hafeez into a drive when he had 15. Hafeez edged a simple catch to Graeme Smith at first slip.
Kallis also got Yasir Hameed to give a faint edge to wicketkeeper Mark Boucher for 9. Kallis ended the day with 2-18 off six overs.
Younis and Farhat batted slowly at first but began to play aggressive strokes, frustrating the South Africa bowlers in their unbroken third-wicket partnership of 45.
Earlier, Prince top-scored for South Africa with his sixth Test century. He was stumped for 138 by Kamran Akmal off the leg-spin bowling of Danish Kaneria just before the lunch break.
It was Prince's second-highest Test score, after his 139 not out against Zimbabwe in 2005 at the same ground. He hit 19 fours in his innings, and batted for 349 minutes to lift South Africa from 53-3.
His dismissal also ended a 213-run fifth wicket partnership with Herschelle Gibbs, who was out for 94 -- the sixth time he had got out in the 90s.
"We needed a big partnership and luckily we got it," Gibbs said. "It helped having [Prince] at the other end."
"[Prince is] hitting the ball better and playing better than I have ever seen him play," Gibbs said.
"We would have liked a lead of about 150 or 200. There'll be a lot of work to do tomorrow. The first session will be very important," Gibbs said.
Kaneria finished with 3-97 and Mohammad Asif, in his first match after being allowed to play after a doping ban, had 5-89.
Shaun Pollock shepherded the South Africa tail with his undefeated 39.
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