At stumps, South Africa were struggling on 245 for eight as no batman could resist against Pakistani bowlers except Hashim Amla and Jean-Paul Duminy.
Amla hit an unbeaten 118, his twentieth Test hundred, and Duminy made 57, his fifth Test half-century.
Amla added 61 for the fourth wicket with AB de Villiers (19), and another valuable 95 for the fifth with Duminy to stop Pakistani bowlers from running away after they had wrecked the top-order.
Just when it looked as though Amla and Duminy would see off the day, left-armer Babar (3-89) struck twice, dismissing Duminy and Faf du Plessis in the space of six runs to bring Pakistan back in the game.
Duminy, who had not played a Test since rupturing his Achilles tendon on the tour of Australia in November last year, hit six fours and a six before sweeping Babar straight into the hands of a deep fine-leg fielder.
Du Plessis edged Babar to slips on one, thrilling the roughly 2,000 fans celebrating the Eid holiday.
Pakistan had looked to Saeed Ajmal for the breakthrough, but the off-spinner looked off colour on his 36th birthday, conceding 57 runs and managing only Vernon Philander's wicket.
Pakistani pacemen Mohammad Irfan (2-42) and Junaid Khan (1-52) had generated lively pace, with Irfan taking two early wickets in the first session.
Irfan, the tallest ever player at seven feet one inch (2.1 metres), lifted one to Alviro Petersen (three), whose fended push was well caught by Shan Masood at short-leg, and then had Graeme Smith for 15 in his fourth over.
Smith, who is playing his first international match since an ankle injury earlier this year, hit Irfan for two well-timed boundaries but the lanky paceman had the last laugh, dismissing the South African skipper caught behind.
Kallis, who is also playing his first Test since February this year, looked rusty before he edged a sharp incoming delivery from Khan for wicket-keeper Adnan Akmal to take a smart low catch.
De Villiers helped Amla take South Africa past the 100-mark before he fell, run out for 19.
Pakistan chose two pacemen and as many spinners, with 34-year old Babar and opener Shan Masood making their debuts.
South Africa entered the match with three frontline pacemen and Peterson as only spinner. (AFP)
