The 30-year-old right hander was unbeaten on 71 as South Africa moved to 152-4 at tea from a precarious 104-4 after winning the toss at Sheikh Zayed Stadium.
At the break Jean-Paul Duminy was the other not out batsman on 36, having added 48 for the unbroken fifth wicket stand with Amla on a day when Pakistan's spin-cum pace attack was on top.
Amla pulled paceman Junaid Khan to the square-leg for his seventh boundary to complete his 28th Test fifty. He has so far batted for 134 balls, hitting eight boundaries.
Irfan, the tallest ever player at 7feet one inch (2.1metres), 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.
South Africa were struggling at 66-3 at lunch.
De Villiers helped Amla take South Africa past 100-mark before he fell in a bizare manner, run out for 19.
De Villiers defended a slower one from spinner Zulfiqar Babar and as the ball rolled to first slip, Younis Khan threw the ball to Akmal who saw the batsman out of his crease dislodged the stumps.
Babar and opener Shan Masood made Test debuts for Pakistan.
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