James Anderson and Mark Footitt had sent down just one over each at the start of the afternoon session when the crack of thunder alerted groundstaff to an imminent downpour.
The teams wisely left the field and within minutes lightning, heavy rain and even hail stones pummelled the ground.
No further play was possible, leaving some of the England attack light on competitive overs. Anderson bowled just five in the match, though at 33 he is happy to work a reduced schedule before Tests, and new-ball partner Stuart Broad managed only 37 balls.
Both men are assured of their places in the series opener in Durban on Boxing Day, meaning the greater frustration lies with the uncapped Footitt and Chris Woakes, who are both eyeing the third seamer’s spot.
Footitt took three wickets to Woakes’ one but was significantly more expensive and his non-appearance with the bat during England’s second innings may suggest the left-armer’s prospects of a debut are receding.
More will be known when England name their side to face South Africa A in Pietermaritzburg on Sunday, when Steven Finn could come into contention if passed fit.
Trevor Bayliss’ side have enjoyed their stay at Senwes Park, home to a well-appointed training complex used by the Spanish football team during their triumphant 2010 World Cup campaign.
The facilities are highly regarded and the altitude helpful for conditioning, but the last day of cricket had already fallen flat before the weather turned.
Resuming their second innings on 99 for three, the tourists lost seven wickets for 91 runs before lunch.
An overnight lead of 381 rendered that collapse moot, with each of their likely top seven spending at least an hour at the crease during the game.
Even Alex Hales, who was dismissed for eight in each innings and has work to do, at least had time in the middle.
But the morning session belonged to Junior Dala, the Zambian seamer who accounted for Hales in each innings.
Dala took four wickets before lunch to finish with five for 34, with Gary Ballance, Joe Root, Woakes and Broad his latest scalps.
Of those, Ballance has most cause for disappointment. He is pencilled in as the reserve batsman on tour but may come into contention should Hales falter and Nick Compton return to the head of the innings. Twenty-five straightforward runs and an ugly dismissal, courtesy of ill-conceived pull at Dala, did not advance his cause much.
Jonny Bairstow was also upset with the manner of his exit – a golden duck – after being caught behind despite no obvious sign of an edge.
England were willing to wait as long as possible to return to the field but, while the rain ceased, the continued presence of lightning made it an unappealing prospect.