The tourists resumed on 126-8 and still required 28 runs to avoid the follow on after Toby Roland-Jones had instigated a stunning batting collapse on Friday (28 July) to continue the feelgood factor provided by a Ben Stokes century that helped the hosts post a first-innings total of 353.
The Middlesex seamer completed a memorable debut five-fer with the wicket of Temba Bavuma, who had notched his eighth Test 50 before being caught behind by Jonny Bairstow.
That left South Africa all out for 175 after James Anderson had made the initial breakthrough by coaxing an edge from Morne Morkel  that flew to Alastair Cook at first slip.
Stokes came within a whisker of producing one of the catches of the year low to his left in the gully, but was just unable to keep hold of a powerful Bavuma edge.
Vernon Philander  was the last man left standing for the Proteas despite having spent the night in hospital on an intravenous drip after a suspected viral infection worsened.
In response, England reached 74-1 before proceedings were halted for the second time in mid-afternoon and eventually abandoned with no further play possible. Cook  did not provide a repeat of his impressive first-innings knock as he was dismissed by Morkel for the 11th time in Test cricket thanks to a corker of a delivery.
Underfire opening partner Keaton Jennings reached 34 after surviving a dropped catch off Philander on six and an initial lbw decision that was overturned on review after replays showed that Kagiso Rabada's ball had pitched outside leg stump. Another of Trevor Bayliss' three debutants, Tom Westley, struck 28 before the covers were rolled back on.
The weather forecast appears brighter for the final two days of action in Kennington and England will hope to be given ample time to wrap up a second victory of what continues to be a very topsy-turvy four-matches series.
Moeen Ali spun Joe Root's men to a thumping 211-run opening win at Lord's, but that emphatic victory was followed by a calamitous and wholly ugly 340-run loss at Trent Bridge. The final contest begins at Old Trafford on 4 August.