England failed to make a breakthrough when rain stopped play before tea on the fourth day of the second Test at Headingley on Sunday as South Africa reached 39 without loss in their second innings.
Jacques Rudolph, opening in place of the injured Alviro Petersen, was unbeaten on 21 while skipper Graeme Smith was on 17 as he continued to bat with a minor knee injury.
Thunder and lightning arrived just minutes after the players left the field with the skies over northern England turning an ominous dark grey.
It was a frustrating passage of play for England, who had failed to capitalise on Kevin Pietersen's exhilarating first innings century that helped the hosts to 425 in reply to the Proteas' 419.
Smith survived a scare before lunch when England reviewed an lbw appeal but it was rejected. Television replays showed the ball would have bounced over the stumps.
Apart from a couple of edges that failed to carry through to the slips the South African openers held their own.
Earlier on Sunday, Pietersen had resumed on 149 with the team on 351 for five.
England had hopes of passing South Africa's first innings and taking a significant lead, but Pietersen was out to the second ball of the morning - lbw to Morne Morkel without adding to his overnight score.
Pietersen's effort threatened to turn the Test on its head on Saturday with a counter-attacking innings that carried England away from potential danger at 173 for four.
It was his 21st Test hundred and came from 214 balls.
Tim Bresnan (9) and Stuart Broad (1) failed to wag and could not stay with Matt Prior (68) and help him to fashion out any kind of significant lead.
Prior advanced his score from 20 overnight before he became the ninth wicket to fall when he swept leg-spinner Imran Tahir to Dale Steyn at fine leg.
James Anderson (8) was the last man out, bowled by Tahir after reverse sweeping the spinner for four the ball before.
England, 1-0 down after losing at the Oval in the first Test, need to avoid defeat in the three-match series to prevent South Africa from leapfrogging them and claiming the number one Test ranking.