West Indies made a terrible start to their reply when Devon Smith, who has made just 22 runs in his last five innings, was caught by Ricky Ponting at second slip with the total on two.
He was soon withdrawn by Smith and South Africa succeeded in stifling the scoring before Jaffer, after a spell of five maiden overs, fell to Ntini for 26 with the total on 61 as de Villiers claimed another slip catch.