There was a wicket apiece for opening pair Dale Steyn and Vernon Philander, with Morne Morkel taking two more as the visitors' top order crumbled under an intense examination.
Younis Khan regained some control to reach the interval on 24 not out, with Asad Sahfiq alongside him on 11no.
The South Africa bowlers got first use of the Cape Town pitch after Graeme Smith won the toss.
The first four overs yielded just one run as Steyn and Philander gave nothing loose and the first wicket was down midway through the eighth over.
Philander first had Nasir Jamshed dropped by Faf du Plessis at gully but dismissed him for three with the very next delivery when AB de Villiers gathered a simple catch behind the stumps.
Mohammad Hafeez scored the first boundary of the day off the 58th ball and moved along to 17 by the time Steyn sent him back with the first ball of his second spell.
A testing line and a hint of away movement produced the edge and Smith took a low catch at slip.
Azhar Ali was then dismissed for four when he aimed an airy drive at Morkel.
Morkel made it 33 for four just four balls later, spearing one at captain Misbah-ul-Haq's body and being rewarded with an awkward fend to Dean Elgar at short-leg.