Amla also becomes the 70,000th wicket to fall in Test cricket.
Bangladesh face a long haul in their bid to fight their way back into contention against South Africa after ending the second day of the first test on 127 for three, still 369 behind the hosts' first innings tally.
Mominul Haque (28) and Tamim Iqbal, who hit a six off the final ball of the day to reach 22, were not out at stumps on Friday as Bangladesh began their reply after South Africa's tea-time declaration on 496 for three.
Visiting captain Mushfiqur Rahim led a spirited charge but fell on 44 from 57 balls after being caught at forward short leg off Keshav Maharaj, who had seen Dean Elgar at first slip spill two earlier chances to snag the Bangladesh skipper.
Mushfiqur's brief spell suggested the possibility of an intriguing contest as a flat track at Senwes Park looked likely to begin offering more turn on the third day on Saturday. Mushfiqur's wicket followed that of openers Imrul Kayes (7) and Liton Das (25), who went early as Kagiso Rabada and Morne Morkel made the breakthrough for the hosts.
Elgar fell one run short of a maiden double century as South Africa battered Bangladesh's bowlers for a second day. They were 298 for one overnight as Elgar made his highest test score and Hashim Amla completed his 27th century before lunch on Friday. Amla became the 70,000th wicket to fall in Test cricket when he was dismissed three balls after lunch, chipping Shafiul Islam straight to Mehidy Hasan at backward point to depart for 137.
Elgar, who seemed to lose concentration as he approached his double ton, skyed a short delivery into the air to be caught by Mominul an agonising single run short of the milestone. On the first day, Elgar saw his new opening partner Aiden Markram run out for 97, heartbreakingly short of a debut ton.
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 "south africa, bangladesh, cricket, test cricket, South Africa v/s Bangladesh, hashim amla, dean elgar, mushfiqur rahim, keshav m")
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