The Royal Swazi Sun course continued to have its par of 72 battered from all sides, with Vaughan leading the assault with a second nine of 29. The 25-year-old from Vanderbijlpark, two shots off the lead overnight, reached the turn at a modest level-par for the day as Scotland's Murray Urquhart climbed to 16-under and the on-course lead with an outward nine of 32.
But Vaughan surged through the field with his back nine of 29, featuring an eagle and five birdies on his way to a 65 and the overall lead at 17-under par 199.
Englishman Mark Hilton, Switzerland's Andre Bossert and South African Hennie Otto are all grouped together at 14-under 202, while Urquhart dropped three shots in his final four holes to finish a stroke back on 203.
'It was absolute carnage out there. There were birdies being made all over the place,' said Vaughan, who struggled with a cold putter on a first nine where he stood the chance of being left behind by Urquhart, Bossert and Otto.
'I missed at least four short birdie putts on the front nine. The whole time I just told myself to keep hitting the ball as well as I was, and just wait for that one putt to drop. I knew it would start a run when it happened.'
Vaughan came close to birdies on holes 10 and 11, but the catalyst was his chip-in from 15 meters for an eagle at the par-five 12th. He went on to birdie five of his next six holes to separate himself from a bunched leaderboard.
'I just had tunnel vision off the tee. I picked my target and that was it. I'm thinking a lot better than in the past. Now that I have a manager, I can focus solely on my golf and not have to worry about other things,' said Vaughan, who has aligned himself with Cape Town-based BMT Sports Management.
'In the past, a frustrating first nine like this would have taken the wind out of my sails. But I've changed all that, and am far more focused and positive on the course.'
Otto made a strong charge for the lead on Saturday. The Boksburg professional was joint leader with Vaughan and Urquhart at 15-under and playing 17. But his efforts were undone by a double-bogey after he hit a sand-wedge fat and into the water guarding the green, making for a disappointing seven amidst three birdies at holes 15, 16 and 18 for a 67.