Khan would need rest for at least four weeks.
He wasn't included in the T20I squad though.
Fast bowler Anrich Nortje has a shoulder injury.
The average first innings score at the venue suggests favourable batting-conditions.
Du Plessis and Quinton de Kock have been rested for the last two encounters.
The three-match series has been completely one-sided thus far.
Obey McCoy has replaced Andre Russell in the squad.
The broadcaster has said that it has already paid a hefty sum for the rest of the tour.
Malan felt he deserved more chances at least in the shortest format.
The squad was decided after discussion with coach Richard Pybus.