Goosen is through three rounds at 7-under-par 212, but he will have stiff competition Sunday in fellow South African Ernie Els, who also shot a 69 Saturday to move into second place at 4 under.
Overnight leader Ross Fisher stumbled to a 78 at the par-73 Fancourt Golf Club and fell into a tie for third place at minus-3. Darren Fichardt joined him there after his second straight 69.
Goosen, the 1995 champion, played in the final threesome with Fisher. But while the overnight leader struggled to bogeys on two of his first three holes, Goosen thrived with a birdie and an eagle by the fifth.
The duo was tied at minus-six after the five-hole stretch, but Fisher moved back to 8 under by the turn. However, he faltered badly with four bogeys and one double bogey on the back nine, to go along with just one more birdie.
Goosen, meanwhile, strung together seven straight pars after his eagle at the fifth. The two-time U.S. Open winner dropped his only shot of the day at the par-5 13th, but finished his round with birdies on 17 and 18 to take his three-shot lead.
'I'm happy to be playing with Ernie tomorrow, I always enjoy it,' Goosen acknowledged. 'It's good for everybody. But this (course) is playing like a majors course, so I'll have to play really solid tomorrow if I'm going to win.'
Els, who returned to competitive golf two weeks ago and won last week's dunhill championship, carded three birdies and a bogey on the front nine.
A three-time winner of this event, Els went on to eagle the par-5 13th, stumbled to a bogey at the 16th and then finished with a birdie at 18 to secure his place in the final threesome.
'It will be great to play with Retief (on Sunday) because it looks like he's playing very well,' said Els, who owns a house on the course. 'It will be special tomorrow for the crowd and the tournament and it will be like a major for us.'
Including Goosen, Els and Fichardt, there were seven South Africans in the top 10 after the third round.
Louis Oosthuizen (69) and Keith Horne (72) were among a group tied for fifth place at 2 under; defending champion Tim Clark (72) was tied for eighth at minus-1; and Charl Schwartzel (75) was among a group tied for 10th place at even-par.
There were just nine players under par heading into the final round.