Rain prevented South Africa from claiming a three-day win over Bangladesh in the first Test, with only 19.2 overs being played on Friday.
The visitors lost two further wickets to reach 67-3, still 221 runs behind South Africa.
The hosts will expect to end the contest on the fourth day as the forecast for Saturday is much better.
Junaid Siddique battled for 100 minutes to rack up 27 runs, before he was eventually removed by Jaques Kallis, playing loosely outside off-stump to edge to wicketkeeper Mark Boucher.
Paul Harris was missing from the host squad, having been sidelined for at least three weeks with a fractured thumb suffered during the match.
The spinner is expected to be available in time for the Test series against Australia in mid-December.
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