Australia reached the lunch break on 311 for seven with Michael Hussey unbeaten on 40 and Warne on 35, the tourists adding 83 runs in the session for the loss of two wickets to paceman Nel.
Resuming on 228-5, Hussey and Andrew Symonds scored just 25 runs in a slow first hour in which the South Africans bowled tightly but could not make the batsmen play often enough.
Both Shaun Pollock and Makhaya Ntini moved the ball off the seam and kept most of their deliveries targeted on the line of off-stump.
However, the batsmen were content to let a majority of deliveries sail harmlessly over the stumps until Nel broke the deadlock with a ball that pitched on Symonds' off-stump and seamed into the right-hander to trap him in front for 13.
Four balls later, Adam Gilchrist cut a delivery from Nel uppishly to point, where Ashwell Prince dived and put both hands on the ball but dropped the catch when his elbows hit the ground.
South Africa were no doubt still ruminating on their seventh dropped catch of the series when Gilchrist failed to move his feet to a ball in Nel's next over and edged a lazy waft to wicketkeeper Mark Boucher to be dismissed without scoring.
Warne's arrival brought an immediate lift to Australia's scoring rate. The leg spinner faced just 27 balls for his runs, and he hit six fours as well as a towering six off left-arm spinner Nicky Boje.
Hussey also hit six fours and a six as the pair put on 52 runs off 62 balls in their unbroken eighth wicket partnership.