Graeme Smith's poor run of form in the series continued as he departed for five, edging Ryan Harris through to wicketkeeper Brad Haddin.
South Africa soon found themselves further in the mire at 42 for two when Dean Elgar (11) was caught behind off James Pattinson.
Alviro Petersen and Hashim Amla staged a mini recovery sharing a 53-run, third-wicket stand.