England lost for a second week as South Africa secured victory by the narrowest of margins.
There were few try scoring opportunities in the opening stages of the Test. England had an early injury scare when Toby Flood took a blow to the head, but he was able to continue after a short break.
Penalties for both sides saw South Africa take a 9-6 lead at half-time.
The Springboks scored the game's only try in the opening two minutes of the second half, Willem Alberts taking the ball over the line.
England had a good chance to get a try back in the 60th minute with a line-out at the 22-metre line, but were unable to convert the play into a try.
Three Owen Farrell penalties in just over ten minutes brought England to within a point of South Africa, but with only two minutes left on the clock, England ran out of time.
England face the world's top-ranked side, New Zealand, next week.