Morne Steyn and Jean de Villiers touched down as a second-half South African barrage broke England's resistance in the first Test in Durban.
England met the Springboks challenge head on at Kings Park and were level at 6-6 at half-time after Owen Farrell and Steyn traded penalties.
South Africa began to gain the upper hand after the break as Steyn and captain De Villiers broke through and the hosts held on despite two more Farrell penalties applying pressure.
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