Clark, who holds a tight margin over Rose in the race for the money title, had two bogeys on his round but countered with an eagle on the last to regain some ground.
Rose started with a birdie on the par-5 second but ran into trouble on the following hole with a double-bogey. The South African Masters champion dropped another shot with a bogey on the 11th but birdied three of the last six holes to remain afoot.
Both golfers struggled early, but will battle until the end to decide the 2001-2002 Sunshine Tour Order of Merit.
The title grants an invitation to the British Open, the World Golf Championships American Express Championship and the World Golf Championships NEC Invitational.
Vaughan got off to a quick start with an eagle on the first and added back-to-back birdies from the fifth. However, he made bogey twice on the front nine to make the turn at 2-under.
'It was a great start to get an eagle on the first, but then I three-putted twice on the front nine and it was a bit disappointing to turn on 2-under,' said Vaughan.
The 26-year-old rebounded on the inward nine at the Leopard Creek Country Club, picking up shots on all three of the remaining par-5s. But his most important hole was the 10th where he saved par after blasting out of a bunker.
'The key hole for me was 10. I made an unbelievable save after being plugged in the bunker. After making that, I managed to play my back nine quite nicely,' said Vaughan. 'Had I hit bogey there, it could have all been all so different. It's very difficult to concentrate in this heat.'
After the bunker shot, Vaughan eagled the 13th and added his third eagle of the day on the last hole.
Vaughan, a three-time winner on the Sunshine Tour, posted his best result this season at the Zimbabwe Open where he finished second to Darren Fichardt.
'I've been trying too hard and the results just haven't come, so I'm trying not to force it,' he said. 'It's been a very frustrating season for me, but I've come here intent on playing more relaxed.'
Nic Henning of South Africa finished alongside Scotland's Doug McGuigan at 6-under 66 while four players were a shot further back, including American Bruce Vaughan. He was joined by the South African pair of Trevor Immelman and Titch Moore and England's Lee Slattery.
The Tour Championship features a field of 72 professionals and three amateurs.
Full-field scores from the South African Tour Championship