Markram made a career-best 70, beating his previous best of 63, and de Kock kept up an outstanding run of form with 60 from 42 balls as South Africa reached 168-4 after winning the toss.
Pakistan won the first test by seven wickets and has not beaten the Proteas in a home test series since 2003.
Du Plessis was on 55 and Bavuma on 41 as stumps were called on Day 2 in Centurion.
Aiden Markram has spoken about the possibility of leading South Africa as the Proteas are currently on a lookout for the position in the longest format.
Cricket South Africa said that the injury took place during Day 2 of the ongoing Test against England and will require surgery which will keep him away from the game for at least six weeks.
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