Playing at the Gary Player Country Club, Vaughan made an eagle at the last to grab the outright lead over Justin Hobday, who came in with a 66 at the Lost City course.
Participants in this event play alternating rounds over the two adjacent courses for the first 36 holes, and then play the final 36 holes at the Gary Player course exclusively.
At 44 years of age, Vaughan has been a regular on the South African Tour for some time. He may not be of great popularity in his homeland of the States, but he has certainly had some success at the game abroad.
He won the Mt. Edgecombe Trophy in 1994 and had two runner-up finishes that year as well, coming at the ICL International and the South African Masters.
And at this tournament, he finished in third place in 1999, and tenth last year.
Today, he chipped in at the par-5 18th for eagle and 65.
'It was going at the right speed, so if it hadn't gone in it would have been an easy birdie,' he said. 'I was just trying to get it up and down.'
Vaughan may not have expected the eagle chip to fall simply because of the conditions of the green. Due to the extreme heat the area has been experiencing, they have become quite dried and crusty.
Said Vaughan: 'It's a shame to see them like this.'
Nevertheless, the eagle chip fell and he will tee off Friday with the outright lead.
Two shots back at 5-under is Michael Archer from England. Coming off a 21st place finish at last week's South African Open, the 35-year-old is merely trying to pick up the pieces of his life following the tragic death of his seven-year-old daughter last year. She passed from a rare chromosome disorder.
'Something like that really puts golf into perspective,' Archer said. 'When you play golf now, you appreciate it's just a game.'