The 31-year-old prince pulled up his pony but was thrown forward head-first to the ground and broke his fall with his hands.
Play was stopped as Harry was left on his knees before he got up apparently unhurt and swapped mounts.
He captained a team in the event held yesterday near Cape Town, in aid of his Sentebale charity which supports underprivileged young people in Lesotho.
As the match came to an end, he tumbled to the ground again this time falling between two other players, the BBC reported.
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Writing a joint message in the official match programme with Sentebale co-founder Prince Seeiso of Lesotho, Harry said the support from the event's backers was "vital".
"The success of our previous five polo events has helped Sentebale make a real difference to the lives of vulnerable children in Lesotho," he said.
"The situation in Lesotho remains critical and every day children continue to lose their parents to the HIV/Aids epidemic.
"Sentebale works to protect and support these children providing them with basic necessities we take for granted: food, shelter, care and access to education."
Harry is currently fifth in line of succession to succeed his grandmother his grandmother, Queen Elizabeth II.