The Springboks endured narrow losses on their European tour to rankings leaders Ireland and France, but were satisfied with the way they were playing and how they were building to their title defence in France next year.
England, runner-up to South Africa at the last World Cup but struggling for any consistency, bulked up its lineout options and predicted it would have an edge in the scrum. But it was beaten up in both set-pieces as the Springboks manhandled the English pack and suffocated the English backs.
Kurt-Lee Arendse scored a try in a sixth consecutive test and Eben Etzebeth rewarded the forwards' effort with a second-half try. Four goalkicks by Faf de Klerk and two dropped goals by Damian Willemse reflected an impressive performance on the scoreboard.
South Africa was up 27-6 and down a man after prop Thomas du Toit was sent off when England finally crossed the tryline in the 71st minute through Henry Slade.
That was about the time England started a remarkable comeback against New Zealand from 19 points down to draw their match last weekend.
But South Africa had too much control and memories of losses on its last three visits to Twickenham to let England breathe again.