South Africa still trail by another 44 runs in reply to India's 187 all out in the first innings.
At the break, Amla was batting on 54 off 110 balls with the help of seven fours. Vernon Philander (13 not out) was giving him company in the middle.
India made a promising start to the second session with some incisive bowling from Ishant Sharma (1/28) and Bhuvneshwar Kumar (3/34).
South Africa crossed 100 in the 40th over, but lost another wicket quickly as Bumrah (2/37) bowled Faf du Plessis (8), who was out shouldering his arms to an inswinging delivery.
In between Amla got two lbw reprieves to go with the one in the morning session. First, in the 35th over (on 33), he was deemed not out off Bhuvneshwar even as the ball seemed to be clipping the leg stump. The decision stayed in his favour on umpire's call.
In the 41st over Amla (on 41) was adjudged lbw off Bhuvneshwar once again, but the batsman went for DRS and it showed the ball was missing off-stump.
Amla added 18 runs with Quinton de Kock (8) who was soon caught behind off Bumrah as South Africa were reduced to 125 for six.
India's fight-back though was cut short as Philander added 18 runs with Amla until tea even as the second new ball is due shortly.
Earlier, nightwatchman Kagiso Rabada frustrated the Indian bowlers for 114 minutes as South Africa reached 81 for 3 in 31 overs at lunch.
Starting from overnight 6/1, Rabada looked to bat for time in a bid to help South Africa an early march on day two.
Finally, in the seventh over of the morning, Bhuvneshwar got his reward as Elgar edged behind off another out-swinger.
Amla then joined Rabada and the duo frustrated India with a 66-run partnership for the third wicket.
To counter his fallibility outside the off-stump, Amla had a massive trigger movement to counter the seam movement as both Bumrah and Mohammed Shami got the ball to jag around.
Rabada didn't look in any trouble whatsoever even as the Indian bowlers were guilty of bowling a tad shorter than Cheteshwar Pujara had underlined after close of play on day one.
They created one major chance to break this partnership as Ishant had a loud leg before shout off Amla turned down in the 28th over.
India went for DRS but the decision stayed in Amla's favour on umpire's call, as the ball seemed to just clip the stumps.
Two overs later though, Ishant got the breakthrough and Rabada was finally out, caught at gully by Ajinkya Rahane.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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