The tourists moved from 31 for one to 108 for two against Kent, in 22 overs following a delayed start because of overnight rain and before a lunchtime storm broke over Canterbury.
Hashim Amla and Jacques Kallis were unbeaten as South Africa took their reply to 210 against a home pace attack comprising seasoned pair Charlie Shreck and Simon Cook as well as England Lions' Matt Coles and 20-year-old Ivan Thomas.
A slow pitch, which meant some hard work for Dale Steyn and company on Friday, gave South Africa's batsmen the opportunity to fine-tune their preparation for the first Test of three against England - which will start at The Oval on Thursday.
All four of the top order who have tried here - captain Graeme Smith was the only man out on Friday night - have made it into the 20s. Smith's fellow opener Alviro Petersen was the batsman to go in the play possible on Saturday morning, lbw pushing forward when Cook got one to hold its line up the slope.
Amla and a fluent Kallis were then untroubled to add an unbroken 34, until the forecast rain arrived with a vengeance.
On leaving the field, South Africa discovered the latest International Cricket Council rankings update has demoted them from second to third behind England - fresh motivation perhaps to try to usurp their hosts at the top of the table once the rain relents this summer.
They can expect to be back on the pitch early on Sunday, if the weather allows. When play was called off shortly after lunch, it was also announced that a 1030am start is planned on a final day which will contain 98 overs.
Assistant coach Russell Domingo is unperturbed by either South Africa's relatively short preparation time before the first Test, or their minor slide in the ICC rankings.
"I reckon if we were here for a month we'd still struggle to get in a lot of preparation," he said, as he surveyed a waterlogged outfield. "I'm not worried. We had such a good week of preparation in Switzerland - the guys were almost saying 'we're mentally ready to play already'. They're fired up to go and do this."