South Africa reached stumps at 382-6 for an overall lead of 205 with four wickets still in hand.
Captain Du Plessis, out for a pair in the first Test in Centurion, steered the hosts to an imposing first innings total by scoring 103 in the company of Bavuma (75) as the two added 156 for the fifth wicket.
The hosts had to counter some accurate bowling before lunch when Pakistan took two wickets. The visitors thought they had a third when Bavuma, on three, edged seamer Mohammad Abbas to Azhar Ali at first slip.
The on-field umpires gave a soft signal of out but asked TV umpire Sunderam Ravi to check whether the catch was clean. The third umpire decided the ball had touched the ground, leaving the Pakistan team and coaching staff in disbelief.
Batting became increasingly difficult with cracks widening on the pitch. The one outside the right-handers’ off stump accounted for the wickets of Aiden Markram and Hashim Amla.
Du Plessis and Bavuma batted cautiously before raising the scoring rate in the middle session. As the day wore on, Pakistan’s seamers lost their pace as Abbas and Amir struggled to touch the 130kph mark at times.
Leg-spinner Yasir Shah was curiously under-used, bowling 21 overs without success for 79 runs. South Africa wicketkeeper Quinton de Kock was unbeaten on 55 when stumps were drawn.
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