Until then, only Matthew Hoggard had gained any tangible reward with the ball, having produced a cracking first over de l ivery that Martin van Jaarsveld could only glove behind.
But Simon Jones and Steve Harmison then combined to give England a hint of hope by removing Andrew Puttick and Justin Ontong in quick succession.
Their only real chance of avoiding defeat, however, rested with the weather. It did its best, too, with a torrential downpour soaking players and outfield alike with the total 101 for three.
This time, play was suspended for 75 minutes. But there was no escape for England - and an over from Jones that cost 21 runs sped Ashwell Prince and Jean-Paul Duminy to the winning line with 30 overs unused.
Losing here would not have been part of the plan when Vaughan's squad assembled in Johannesburg last week. But it is the performances of several key players that must concern England far more as they prepare to head for Port Elizabeth.
Vaughan, 82 overnight, completed his century as he and the tail tried to make something out of a down and almost out second innings total of 154 for seven. But everyone knew the captain was in decent form anyway after his good sequence of scores in Zimbabwe.
It's players like Mark Butcher, Graham Thorpe, Andrew Flintoff and Harmison - who didn't make the trip to Harare and had not battedor bowled in anger for two months or more - who are struggling for runs and rhythm.
Even Vaughan failed to kick on quite as he would have hoped today. After reaching exactly 100 - from 158 balls with a couple of sixes and 13 fours - he chased a wide delivery from Charl Willoughby to edge a catch behind.
Having totalled 225 in their first innings, England were all out for 190 second time around.
Butcher is the biggest concern. He has not batted in a Test since mid-June because of injuries and accidents and three find-your-feet innings on this tour have spanned just 29 balls and yielded nine runs.
There is still time before Friday for England to change their mind and plump for Rob Key in Port Elizabeth but it would be a surprise if England switched horses at this stage.
