South Africa's Tjaart van der Walt posted a 6-under-par 66. Tim Clark, the 2002 champion, joined fellow South Africans Charl Schwartzel and Des Terblanche at 4-under-par 68 along with the English duo of Malcolm Mackenzie and Chris Williams, and Norway's Lars Brovold.
Moore started on the back side and collected his first birdie of the day at the par-4 13th. Moore then hit a tremendous drive at the par-5 14th and dropped his approach inside 6 feet for an eagle.
The South African added back-to-back birdies from the 17th to make the turn at 5 under. He then birdied the par-5 third, but found trouble with a bogey at the par-4 fifth.
Moore responded well and birdied the eighth and ninth holes to close his round alongside Vaughan.
'You have to play well here but a lot of it is about patience as well,' said the 28-year-old Moore. 'There are a lot of birdie holes out there but you have to take your pars where you can get them too.'
Vaughan, an American journeyman who turned pro in 1982, ran off four birdies on the back nine to get his round going. He stumbled around the turn with a bogey at the first but countered with a birdie at the very next hole.
The 48-year-old then tallied three consecutive birdies starting at the par-4 sixth for his share of first.
'I am more shocked than anybody else being up there, because the only thing I have been able to do at home is putt but I putted pretty well today so I guess that has paid off,' said Vaughan, who has undergone numerous surgeries over the past two years to treat his ailing left knee.
Gregory Havret, Marcel Siem, Philip Golding, Louis Oosthuizen, Andrew McLardy, Ross Wellington and Lindani Ndwandwe are tied for 10th place at 3-under-par 69.
Two-time defending champion Trevor Immelman was one shot further back in a group at 2-under-par 70.
Darren Clarke, who is making his first start since November after taking time off to be with his wife, who is dealing with cancer, carded an even-par 72 to finish seven shots off the pace.