Virat Kohli (39 batting) and Murali Vijay (31 batting) were at the crease for India, who earlier in the morning session bowled out the hosts for 335. The visitors trailed South Africa by 255 runs at tea.
While opening batsman Rahul gave a return catch to Morkel following a soft drive, Pujara ran himself out as he hurried for a run on the first delivery he faced. Debutant Lungi Ngidi's direct throw from mid-on caught Pujara short of the crease and India received a big blow.
But Kohli's excellent attacking batsmanship, with his 39 coming off 51 balls, and Vijay's dogged and patient approach not only kept the hosts at bay but also applied the pressure on them.
Kohli played with a clear mind of presenting a straight bat against the South African bowlers who were inconsistent with their probing line and length. When they erred, Kohli made full use of it, especially the ones pitched higher up.
He also used his wrists well to employ flicks off Kagiso Rabada and Morkel. South Afria opened up the infield, allowing the Indians to also get singles.
Vijay, at the other end, batted with patience, backing his defensive techniques to the hilt. He fended off the rising delivery outside the off stump with controlled cut and push.
Brief scores: South Africa first innings: 335 all out (Aiden Markram 94, Hashim Amla 82, Faf du Plessis 63; Ravichandran Ashwin 4/113, Ishant Sharma 3/46) vs India first innings: 80/2 (Virat Kohli 39 batting; Morne Morkel 1/24) at tea on Day 2.
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