The 30-year-old’s knock of 118 in a total of 245 for eight was the stand-out performance on a day when the Proteas failed to make the most of winning the toss.
Amla, currently ranked the best Test batsman in the world, began fighting a rearguard action as early as the third over and remained resilient throughout with JP Duminy (57), in his first Test innings in over a year, the only other batsman to score more than 19.
The pair shared a fifth-wicket stand of 95 to change South Africa’s fortunes after they had slipped to 104 for four. Amla faced 250 deliveries, having been in the middle for all-but 17 balls of 90 overs bowled in the day, and struck 13 boundaries, bringing up his 20th Test century after tea off 201 balls.
Duminy was more aggressive, hitting a six and five fours in 94 balls, but eventually fell in the final session to give Zulfiqar Babar a first wicket on his Test debut.
The slow left-armer went on to claim two further victims, Faf du Plessis and Robin Peterson falling in quick succession, but neither he nor Pakistan’s best bowler Mohammad Irfan could dislodge Amla.
Vernon Philander fell late in the day, pinned lbw by Saeed Ajmal having unsuccessfully asked for the decision to be reviewed by the third umpire, leaving Dale Steyn (13no) to accompany Amla to the close.