The match was reduced to nine overs per side and South Africa were led by a spectacular 47 not out from Hashim Amla as they notched up 77 for five wickets.
Steven Finn took two for 17 from his two overs as the batsmen and fielding side struggled in the greasy conditions, Jacques Kallis (13 not out) helping to boost the score at the end with a seven-ball cameo.
The rain showed no sign of abating as England's batsmen took the field and they never got going, opener Craig Kieswetter swiping desperately at Morne Morkel's first over.
England were 29 for two off 4.1 overs when the umpires, aware that five balls were required to force a result under the Duckworth-Lewis method, called the players off the field.
South Africa won the first match on Saturday and can seal a series victory in the third game on Wednesday ahead of the Sept. 18-October 7 Twenty20 World Cup in Sri Lanka.