The Proteas were 188-5 in their second innings, with a lead of 48 runs, when the players were forced from the field for the last time.
Tumi Sekhukhune (33*) and Marizanne Kapp (43*) were at the crease, having stabilised the Proteas innings after they had been in trouble at 118-5.
Kate Cross starred with the ball for England, taking 4-63 in her 17.4 overs.