The Indian captain looked solid during his innings of 54 as he hit five fours facing 97 balls before left-arm seamer Beuran Hendricks sent him back at the stroke of tea time after an 86-run second wicket stand with Ajinkya Rahane (25 batting).
Earlier, South Africa finished their first innings on a healthy 341 after being down in the dumps at 97 for six. Wayne Parnell (91) and Simon Harmer (96) added 186 runs for the seventh wicket to take the Proteas to a position of safety.
Harmer, who is primarily an off-spinner was more attacking as he hit 13 fours and a six in his 168-ball knock before left-arm spinner Shahbaz Nadeem trapped him leg before.
Pandey (3/67 from 24 overs) and Nadeem (3/99 from 30 overs) performed well while Siddharth Kaul and Perveez Rasool also got two wickets apiece.
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Starting the day at 231 for six, Parnell and Harmer batted for a further 18 overs as they took the score to 283 before Harmer was finally sent back by Nadeem. In his next over Jharkhand left-arm spinner sent back Kyle Abbott.
Brief Scores (At Tea):
South Africa A 341 in 121 overs (Wayne Parnell 91, Simon Harmer 96, Ishwar Pandey 3/67, Shahbaz Nadeem 3/99).
India 95/2 in 26 overs (Cheteshwar Pujara 54, Hendricks 2/23).