The second session was a particularly good one for Rahat Ali, bringing him his second and third Test wickets as the Centurion pitch helped him with just enough lateral movement.
Hashim Amla had been the mainstay of the South African first innings with a classy 92 filled with some great strokes that brought him 13 fours, but Rahat removed him with a wide delivery that was edged to wicketkeeper Sarfraz Ahmed as the Bearded Wonder went on the slash.
It was a stirring fightback by Pakistan after lunch as they claimed three wickets for 97 runs in 26 overs, leaving South Africa in a sticky situation.
Amla and Faf du Plessis had been excellent in adding 66 for the third wicket to lift South Africa to 104 for two at lunch and were looking to crack on the pace after the break.
But Du Plessis would be gone in the fourth over of the session, caught behind for 29 off a fine delivery from Ehsan Adil that was back-of-a-length and nipped away.
AB de Villiers was quickly into his stride as he and Amla added 79 for the fourth wicket off just 112 balls but Pakistan would be the happier side at tea as Rahat struck twice in two overs.
Dean Elgar came to the crease when Amla left and only lasted seven balls when he was trapped in the crease by a Rahat inswinger, wasting a review to compound his error.
When South Africa return for the final session, much will depend on De Villiers, who had gone untroubled to 40 not out.
Much was asked of Robin Peterson in Cape Town and he delivered superbly, but South Africa need another contribution from him as well as he resumes on two not out.
To win the toss, bat first and be bowled out on the first day is not going to please captain Graeme Smith, and he will be looking to his lower-order to help De Villiers steer them to 300 before stumps with the loss of as few more wickets as possible.
The grossly inexperienced Pakistan pace attack were beginning to feel the strain at lunch as Amla and Du Plessis cruised along.
The Pakistanis had claimed two early wickets as the openers, Alviro Petersen (10) and Graeme Smith (5), fell cheaply in the first 10 overs.
The visitors had made two changes to their pace attack with Umar Gul unwell and Tanvir Ahmed dropped. With Junaid Khan still feeling the effects of the strange thigh wound that kept him out of the second Test in Cape Town, the Pakistanis brought in Rahat and debutant Adil.
That left Mohammad Irfan, who made his debut in Cape Town, as the leader of the attack, while Rahat had also played his first Test just 10 days earlier at the Wanderers.
It was Rahat who made the first breakthrough, trapping Petersen lbw for 10, although he had been innocuous up till then.
Petersen’s form may be one of the few items up for discussion in terms of selection, but he had looked good, stroking two boundaries, before receiving a fine delivery from the left-armer (practically his only one of the morning) that straightened sharply back into him.
Smith was less convincing as he scored his five off 21 balls, before he was dismissed in Adil’s first over in Test cricket, edging into the slips, where second slip Younis Khan dived in front of first slip to take the catch. It was a good delivery just outside off stump that bounced a bit more than expected, but Smith’s angled bat towards midwicket was as much to blame as anything else.
South Africa were in some bother at 38 for two, but Amla came in and immediately started middling the ball. He fed off the left-armer’s deliveries angled into him, scoring freely on the leg-side, and reached his 27th Test half-century in the over before lunch, in 102 minutes off 76 balls, with nine fours.
Du Plessis also looked in fine form as he went to 29, collecting three magnificent fours – through the covers, straight and square on the off side – in Adil’s fourth and last over of the morning.
With the inexperienced seamers struggling to regain the upper hand, off-spinner Saeed Ajmal was introduced in the 18th over, but both Amla and Du Plessis continued to score with freedom, using their feet well, and purring along to their 50 partnership off just 74 balls.
With the early moisture having been burnt off and the green tinge gradually disappearing from the pitch, the table is set for the South African batsmen to prosper, even in the absence of Jacques Kallis.
The master batsman injured a calf muscle on Thursday, on one of the rare occasions he attends optional training, and has been replaced by Kyle Abbott, the in-form Dolphins seamer who will earn his first Test cap after excelling in the Sunfoil Series with 49 wickets.