England lost for a second week as South Africa secured victory by the narrowest of margins.
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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.
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