Skipper Mushfiqur Rahim, who was struck a disgusting blow on the side of his head, was out to the last ball of the session, trapped lbw by Wayne Parnell a decision that required ratification by the TV official after Mushfiqur had referred the on field decision.
Mushfiqur was struck with the second ball of the 14th over by Duanne Olivier and required treatment for almost 10 minutes.
Amla went to 100 with a four and from just 113 deliveries, registering a 28th Test century to move past Graeme Smith and into second place alone on the all-time list of South Africa century-makers in test cricket.
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Both Du Plessis and Amla brought up their centuries during their epic stand, but it the end, the partnership was broken when Amla was clean bowled by Subashis Roy for 132, which came off 163 balls and included 17 boundaries. In the first four sessions of the Test, South Africa made 126-0, 130-1, 172-2 and 102-0.
Quick bowler Kagiso Rabada took 5-33 for South Africa and fellow seamer Duanne Olivier had 3-40.
Mominul Haque was hit by a bouncer from Rabada two balls before hooking the same bowler to be caught at deep square leg for 11, while Mahmudullah was hit by Olivier before he had scored.
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So nasty were South Africa with the short stuff that three of Bangladesh's batsmen were hit on the helmet. In the first game, South Africa made 496-3 declared in response.
Soumya Sarkar never looked at ease since walking out in the morning and was undone by yet another unnecessary poke at a ball in the channel outside his off-stump as Faf du Plessis pouched the edge safely in front of first slip.
Rabada took over from that point as he sent Imrul Kayes packing for 26 before slicing through the lower order easily. However, the 334 runs Bangladesh need to make the home side bat again seems too far fetched a hope.
Bulgaria 0 France 1
It's more than a goal, it's a fact, ' added Mbappe, who wasn't born until five years after the defeat to Bulgaria in 1993. Steven Zuber scored twice in Basel as Switzerland made it nine wins from nine by thrashing Hungary 5-2.