Only 26 balls were possible after lunch before the rain set in, long enough for another wicket to fall and for New Zealand to get the new ball.
However, the weather had cleared by the tea adjournment and play was expected to resume in the third session.
Just as he did in the second Test in Wellington where his first-innings 91 set up South Africa's eight-wicket victory, de Kock provided staunch resistance.
Apart from de Kock, du Plessis (53) and Hashim Amla (50) also posted half centuries but the remaining South African batsmen have struggled against a patched-up New Zealand attack.
Recalled quick Matt Henry and medium pacer Colin de Grandhomme, operating in place of the injured Tim Southee and Trent Boult, have four for 57 and two for 52 respectively.
In the morning session, extended by 30 minutes to make up for time lost on day one, South Africa resumed at 123 for four and added 120 runs for the loss of three wickets.
Tom Latham pulled off a stunning one-handed catch to remove du Plessis.
He anticipated the South African skipper was lining up to sweep left-arm spinner Mitchell Santner and was already leaping to his right before the ball was hit.
Latham was again in the action, taking a catch low down at second slip when Vernon Philander on 11 edged a swinging Henry delivery.
After a brief rain delay after lunch, Neil Wagner fired in a short ball to Keshav Maharaj whose attempt to fend it away was gloved through to BJ Watling behind the stumps.
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